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urls.py
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urls.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of the `pypath` python module
#
# Copyright 2014-2023
# EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University
#
# Authors: see the file `README.rst`
# Contact: Dénes Türei (turei.denes@gmail.com)
#
# Distributed under the GPLv3 License.
# See accompanying file LICENSE.txt or copy at
# https://www.gnu.org/licenses/gpl-3.0.html
#
# Website: https://pypath.omnipathdb.org/
#
import os
import pypath.share.common as common
import pypath.share.cache as cache
import pypath.share.settings as settings
urls = {
'uniprot_pdb': {
'label': 'Getting PDB IDs of 3D structures for UniProtIDs',
'url': 'https://ftp.uniprot.org/pub/databases/uniprot/'
'current_release/knowledgebase/complete/docs/pdbtosp.txt'
},
'uniprot_basic': {
'label': 'URL for UniProt queries',
'url': 'https://rest.uniprot.org/uniprotkb/stream',
'lists': 'https://legacy.uniprot.org/uploadlists/',
'datasheet': 'https://rest.uniprot.org/uniprotkb/%s.txt',
'history': 'https://rest.uniprot.org/unisave/%s?format=tsv&version=*',
'deleted_sp': 'https://ftp.expasy.org/databases/uniprot/'
'current_release/knowledgebase/complete/docs/delac_sp.txt',
'deleted_tr': 'https://ftp.expasy.org/databases/uniprot/'
'current_release/knowledgebase/complete/docs/delac_tr.txt.gz',
'speindex_old': 'ftp://ftp.uniprot.org/pub/databases/uniprot/'
'knowledgebase/docs/speindex.txt',
'speindex': 'https://ftp.expasy.org/databases/uniprot/current_release/'
'knowledgebase/complete/docs/speindex.txt',
'taxids_old': 'https://www.uniprot.org/taxonomy/?query='
'*&format=tab&force=true&columns=id&compress=yes',
'taxids': 'https://rest.uniprot.org/taxonomy/stream?compressed=true'
'&fields=id%2Ccommon_name%2Cscientific_name'
'&format=tsv&query=%28%2A%29',
'speclist': 'https://ftp.uniprot.org/pub/databases/uniprot/'
'current_release/knowledgebase/complete/docs/speclist.txt',
},
'uniprot_idmapping': {
'run': 'https://rest.uniprot.org/idmapping/run',
'poll': 'https://rest.uniprot.org/idmapping/status/%s',
'details': 'https://rest.uniprot.org/idmapping/details/%s',
'fields': 'https://rest.uniprot.org/configure/idmapping/fields',
},
'corum': {
'label':
'CORUM is a database of protein complexes, downloadable in csv format',
'url_old':
'http://mips.helmholtz-muenchen.de/genre/proj/corum/allComplexes.csv',
'url': 'http://mips.helmholtz-muenchen.de/corum/download/'
'allComplexes.txt.zip',
'url_rescued':
'https://rescued.omnipathdb.org/CORUM_allComplexes.txt.zip',
},
'pfam_pdb': {
'label': 'PDB-Pfam mapping and names of Pfam domains',
'url': 'ftp://ftp.ebi.ac.uk/pub/databases/Pfam/mappings/'
'pdb_pfam_mapping.txt',
},
'pfam_up': {
'label': 'Mapping Pfam regions to UniProt',
'url': 'ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/'
'Pfam-A.regions.tsv.gz',
},
'3dcomplex_contact': {
'label': 'This file contains the topology '
'definition of the complexes',
'url_old': 'http://shmoo.weizmann.ac.il/elevy/3dcomplexV4/dataV4/'
'contactDefinition.txt',
'url': 'http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/dataV6/'
'contactDefinition.txt',
},
'3dcomplex_correspondancy': {
'label': 'This is the dictionary of chain names',
'url_old': 'http://shmoo.weizmann.ac.il/elevy/3dcomplexV4/dataV4/'
'pdb_chain_corresV2.txt',
'url': 'http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/dataV6/'
'chainDefinition.txt',
},
'pdb_chains': {
'label': 'Corresponding UniProt IDs and residue numbers '
'for each chain in PDB structures',
'url': 'ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/flatfiles/'
'tsv/pdb_chain_uniprot.tsv.gz',
},
'complex_portal': {
'label': 'Complexes curated by IntAct',
'url': 'ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/'
'current/psi25/',
},
'pisa_interfaces': {
'label': 'Base URL for download interface data from PDBe PISA',
'url': 'http://www.ebi.ac.uk/pdbe/pisa/cgi-bin/interfaces.pisa?'
},
'catalytic_sites': {
'label': 'Catalytic Site Atlas',
'url': 'http://www.ebi.ac.uk/thornton-'
'srv/databases/CSA/downloads/CSA_2_0_121113.txt',
},
'3did_ddi': {
'label': 'Domain-domain interactions derived from 3D structures',
'url': 'http://3did.irbbarcelona.org/download/current/3did_flat.gz'
},
'3did_dmi': {
'label': 'Domain-motif interactions from 3DID',
'url': 'http://3did.irbbarcelona.org/download/current/'
'3did_dmi_flat.gz',
},
'swissprot_full': {
'label': 'Full UniProt/Swissprot database',
'url': 'ftp://ftp.ebi.ac.uk/pub/databases/Pfam/'
'current_release/uniprot_sprot.dat.gz',
},
'instruct_human': {
'label':
'Protein interactome networks annotated to 3D structural resolution',
'url': 'http://instruct.yulab.org/download/sapiens.sin',
},
'i3d_human': {
'label': 'Interactome3D representative dataset for human proteins',
'url': 'http://interactome3d.irbbarcelona.org/user_data/human/'
'download/representative/interactions.dat',
},
'instruct_offsets': {
'label': 'Offsets between PDB chains and UniProt sequences',
'url': 'http://instruct.yulab.org/download/indexing_uniprot2pdb.txt'
},
'compleat': {
'label': 'Curated and inferred complexes from multiple databases',
'old_url': 'http://www.flyrnai.org/compleat/ComplexDownload'
'?requestType=complexDownload&org=Human',
'rescued': 'https://rescued.omnipathdb.org/compleat.tsv',
},
'switches.elm': {
'label': 'Curated data on molecular switches in cellular regulation',
'url': 'http://switches.elm.eu.org/downloads/switches.ELM-v1.txt'
},
'ols': {
'label': 'WSDL interface for the Ontology Lookup Service',
'url_wsdl': 'http://www.ebi.ac.uk/ontology-lookup/OntologyQuery.wsdl',
'url': 'https://www.ebi.ac.uk/ols/api/ontologies',
},
'comppi': {
'label': 'Compartmentalized PPI database',
'url': 'http://comppi.linkgroup.hu/downloads'
},
'elm_int': {
'label': 'Interactions between ELM instances and globular domains',
'url': 'http://elm.eu.org/interactions/as_tsv'
},
'elm_depr': {
'label': 'Deprecated ELM class names',
'url': 'http://elm.eu.org/infos/browse_renamed.tsv'
},
'pdbsws': {
'label': 'PDB-UniProt residue level mapping',
'url': 'http://www.bioinf.org.uk/cgi-bin/pdbsws/query.pl'
},
'pdb_align': {
'label': 'PDB-UniProt residue level mapping',
'url_old': 'http://pdb.org/pdb/rest/das/pdb_uniprot_mapping/'
'alignment?query=',
'url': 'https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/',
},
'pepcyber': {
'label': 'MySQL injection to PEPCyber website :)',
'url': 'http://www.pepcyber.org/PPEP/search_result.php'
'?domain=Any&ppbd_symbol=Any&search_field=symbol&'
'query_value=%27+OR+1&binding_sequence=&go_id=Any&'
'Submit=Search',
'rescued': 'https://rescued.omnipathdb.org/'
'pepcyber_search_result.html',
'details': 'http://www.pepcyber.org/PPEP/idetail.php?iid=%u',
'details_rescued': 'https://rescued.omnipathdb.org/pepcyber_details/'
'pepcyber_%u.html',
},
'pdzbase': {
'label': 'Manually curated interactions of PDZ domain proteins',
'url_rescued': 'http://rescued.omnipathdb.org/PDZBase.html',
'url': 'http://abc.med.cornell.edu/pdzbase/allinteractions',
},
'pdz_details': {
'label': 'Details of interactions in PDZbase',
'url': 'http://abc.med.cornell.edu/pdzbase/interaction_detail/%u'
},
'psite_reg': {
'label': 'PhosphoSite annotated regulatory sites',
'url_old': 'http://www.phosphosite.org/downloads/Regulatory_sites.gz',
'url': 'https://rescued.omnipathdb.org/phosphosite/'\
'Regulatory_sites.gz',
},
'psite_bp': {
'label': 'PhosphoSite kinase substrates in BioPAX format',
'url_old': 'http://www.phosphosite.org/downloads/'\
'Kinase_substrates.owl.gz',
'url': 'https://rescued.omnipathdb.org/phosphosite/'\
'Kinase_substrates.owl.gz',
},
'psite_ac': {
'label': 'PhosphoSite acetylation sites',
'url_old': 'http://www.phosphosite.org/downloads/'\
'Acetylation_site_dataset.gz',
'url': 'https://rescued.omnipathdb.org/phosphosite/'\
'Acetylation_site_dataset.gz',
},
'psite_kin': {
'label': 'PhosphoSite kinase-substrate interactions',
'url_old': 'http://www.phosphosite.org/downloads/'\
'Kinase_Substrate_Dataset.gz',
'url': 'https://rescued.omnipathdb.org/phosphosite/'\
'Kinase_Substrate_Dataset.gz',
},
'psite_me': {
'label': 'PhosphoSite methylation sites',
'url_old': 'http://www.phosphosite.org/downloads/'\
'Methylation_site_dataset.gz',
'url': 'https://rescued.omnipathdb.org/phosphosite/'
'Methylation_site_dataset.gz',
},
'psite_ga': {
'label': 'PhosphoSite O-GalNAc sites',
'url_old': 'http://www.phosphosite.org/downloads/'\
'O-GalNAc_site_dataset.gz',
'url': 'https://rescued.omnipathdb.org/phosphosite/'
'O-GalNAc_site_dataset.gz',
},
'psite_gl': {
'label': 'PhosphoSite O-GlcNAc sites',
'url_old': 'http://www.phosphosite.org/downloads/'\
'O-GlcNAc_site_dataset.gz',
'url': 'https://rescued.omnipathdb.org/phosphosite/'\
'O-GlcNAc_site_dataset.gz',
},
'psite_p': {
'label': 'PhosphoSite phosphorylation sites',
'url_old': 'http://www.phosphosite.org/downloads/'\
'Phosphorylation_site_dataset.gz',
'url': 'https://rescued.omnipathdb.org/phosphosite/'\
'Phosphorylation_site_dataset.gz',
},
'psite_sm': {
'label': 'Sumoylation sites',
'url_old': 'http://www.phosphosite.org/downloads/'\
'Sumoylation_site_dataset.gz',
'url': 'https://rescued.omnipathdb.org/phosphosite/'\
'Sumoylation_site_dataset.gz',
},
'psite_ub': {
'label': 'Ubiquitination sites',
'url_old': 'http://www.phosphosite.org/downloads/'\
'Ubiquitination_site_dataset.gz',
'url': 'https://rescued.omnipathdb.org/phosphosite/'\
'Ubiquitination_site_dataset.gz',
},
'proteomic_ielm': {
'label': 'Proteomic iELM',
'url': 'http://i.elm.eu.org/test_submit/'
},
'ielm_domains': {
'label': 'List of domains form iELM',
'url': 'http://i.elm.eu.org/domains/'
},
'domino': {
'label': 'Domino PPI and domain-motif database in MI-TAB format',
'url': 'ftp://mint.bio.uniroma2.it/pub/domino/release/mitab/'
'2009-10-22/2009-10-22-domino-full-binary.mitab26',
'rescued': 'http://rescued.omnipathdb.org/'\
'domino_2009-10-22-full-binary.mitab26.gz',
},
'hprd_all': {
'label': 'HPRD all data in flat files',
'url': 'http://www.hprd.org/RELEASE9/HPRD_FLAT_FILES_041310.tar.gz',
'url_rescued': 'https://rescued.omnipathdb.org/'
'HPRD_FLAT_FILES_041310.tar.gz',
'ptm_file': 'FLAT_FILES_072010/POST_TRANSLATIONAL_MODIFICATIONS.txt',
'int_file': 'FLAT_FILES_072010/BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt'
},
'p_elm': {
'label': 'phosphoELM',
'url':
'http://phospho.elm.eu.org/dumps/phosphoELM_vertebrate_latest.dump.tgz',
'psites': 'phosphoELM_vertebrate_'
},
'p_elm_kin': {
'label': 'List of kinases from phosphoELM',
'url': 'http://phospho.elm.eu.org/kinases.html'
},
'elm_inst': {
'label': 'List of ELM instances',
'url_old': 'http://elm.eu.org/elms/browse_instances.tsv?q=*',
'url': 'http://elm.eu.org/instances.tsv?q=*',
},
'elm_class': {
'label': 'List of ELM classes',
'url_old': 'http://elm.eu.org/elms/browse_elms.tsv',
'url': 'http://elm.eu.org/elms/elms_index.tsv',
},
'dbptm_benchmark': {
'label': 'dbPTM is a PTM database compiled from multiple other dbs',
'urls': [
'http://dbptm.mbc.nctu.edu.tw/Benchmark/N-linked_Glycosylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/N6-succinyllysine.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/O-linked_Glycosylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/Phosphorylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/Phosphorylation_CDK1.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/Phosphorylation_CK2.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/Phosphorylation_MAPK1.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/Phosphorylation_PKA.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/Phosphorylation_PKC.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/S-nitrosylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/Amidation.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/Hydroxylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/Acetylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/Benchmark/Methylation.tgz'
]
},
'dbptm': {
'label': 'dbPTM is a PTM database compiled from multiple other dbs',
'urls': [
'http://dbptm.mbc.nctu.edu.tw/download/N-linked.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/O-linked.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/C-linked.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/Phosphorylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/Acetylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/Methylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/Myristoylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/Palmitoylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/Prenylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/Carboxylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/Sulfation.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/Ubiquitylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/Sumoylation.tgz',
'http://dbptm.mbc.nctu.edu.tw/download/Nitrosylation.tgz',
],
'url': 'http://dbptm.mbc.nctu.edu.tw/download/experiment/%s.txt.gz',
'datasets': [
'Phosphorylation',
'Acetylation',
'Ubiquitination',
'Succinylation',
'Methylation',
'Malonylation',
'N-linkedGlycosylation',
'O-linkedGlycosylation',
'Sumoylation',
'S-nitrosylation',
'Glutathionylation',
'Amidation',
'Hydroxylation',
'PyrrolidoneCarboxylicAcid',
'Glutarylation',
'Palmitoylation',
'Gamma-carboxyglutamicAcid',
'Crotonylation',
'Oxidation',
'Myristoylation',
'C-linkedGlycosylation',
'Sulfation',
'Formylation',
'Citrullination',
'GPI-anchor',
'Nitration',
'S-diacylglycerol',
'Carboxylation',
'Lipoylation',
'Carbamidation',
'Neddylation',
'Pyruvate',
'S-linkedGlycosylation',
],
'old_table': 'http://rescued.omnipathdb.org/old_dbptm.tab',
},
'phosnw': {
'label': 'Human kinase-substrate relationships and phosphosites',
'url': 'http://phosphonetworks.org/download/highResolutionNetwork.csv'
},
'kegg_pws': {
'label': 'KEGG Pathways and KEGG MEDICUS',
'list_url': 'http://www.genome.jp/kegg/pathway.html',
'kgml_url':
'http://www.kegg.jp/kegg-bin/download?entry=%s&format=kgml',
'biopax_l3': 'http://www.pathwaycommons.org/archives/PC2/'
'v8/PathwayCommons.8.kegg.BIOPAX.owl.gz',
'kgml_url_2': 'http://rest.kegg.jp/get/%s/kgml',
'medicus': 'ftp://ftp.genome.jp/pub/kegg/medicus/network/network',
'dbget': 'https://www.kegg.jp/dbget-bin/www_bget?%s',
'pw_annot': 'https://www.pathwaycommons.org/archives/PC2/v12/'
'PathwayCommons12.kegg.uniprot.gmt.gz',
},
'kegg_api': {
'label': 'KEGG API',
'url': 'https://rest.kegg.jp/%s'
},
'pathbank': {
'label': 'A functional annotation and process description network '
'database.',
'pw_annot': 'https://pathbank.org/downloads/'
'pathbank_all_proteins.csv.zip',
},
'depod': {
'label': 'Dephosphorylation substrates and sites',
'urls': [
'http://depod.bioss.uni-freiburg.de/download/DEPOD_201408'
'_human_phosphatase-substrate.txt',
'http://depod.bioss.uni-freiburg.de/download/DEPOD_201405'
'_human_phosphatase-substrate.mitab'
]
},
'mimp': {
'label': 'Kinase-substrate relationships',
'url': 'http://mimp.baderlab.org/fetch_data/phosphorylation_data'
'.tab/phosphorylation_data.tab'
},
'unip_iso': {
'label': 'Isoform sequences from UniProt',
'url_old': 'ftp://ftp.uniprot.org/pub/databases/uniprot/'
'current_release/knowledgebase/complete/'
'uniprot_sprot_varsplic.fasta.gz',
'url': 'ftp://ftp.expasy.org/databases/uniprot/current_release/'
'knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz',
},
'kinclass': {
'label': 'Kinase families and groups',
'url': 'http://kinase.com/static/colt/data/human/kinome/'
'tables/Table%20S2.txt',
'rescued': 'https://rescued.omnipathdb.org/kinase.com__Table_S2.txt',
},
'protdb_exp': {
'label': 'Expression data from ProteomicsDB',
'url': 'https://www.proteomicsdb.org/proteomicsdb/logic/api/'
'proteinexpression.xsodata/InputParams(PROTEINFILTER='
'%%27%s%%27,MS_LEVEL=%u,TISSUE_ID_SELECTION=%%27%%27,'
'TISSUE_CATEGORY_SELECTION=%%27tissue;fluid%%27,SCOPE_SELECTION=%u,'
'GROUP_BY_TISSUE=1,CALCULATION_METHOD=0,EXP_ID=-1)/Results?'
'$select=UNIQUE_IDENTIFIER,TISSUE_ID,TISSUE_NAME,TISSUE_SAP_SYNONYM,'
'SAMPLE_ID,SAMPLE_NAME,AFFINITY_PURIFICATION,EXPERIMENT_ID,'
'EXPERIMENT_NAME,EXPERIMENT_SCOPE,EXPERIMENT_SCOPE_NAME,PROJECT_ID,'
'PROJECT_NAME,PROJECT_STATUS,UNNORMALIZED_INTENSITY,'
'NORMALIZED_INTENSITY,MIN_NORMALIZED_INTENSITY,'
'MAX_NORMALIZED_INTENSITY,SAMPLES&$format=json',
'subs': ['uniprot', 'ms_level', 'scope']
},
'protdb_tis': {
'label': 'Get all tissues where a given protein is expressed',
'url': 'https://www.proteomicsdb.org/proteomicsdb/logic/api/'
'proteinspertissue.xsodata/InputParams(TISSUE_ID='
'%%27%s%%27,CALCULATION_METHOD=0,SWISSPROT_ONLY=%u,'
'NO_ISOFORM=%u)/Results?$select=ENTRY_NAME,UNIQUE_IDENTIFIER,DATABASE,'
'PROTEIN_DESCRIPTION,PEPTIDES,SAMPLE_NAME,SAMPLE_DESCRIPTION,'
'UNNORMALIZED_EXPRESSION,NORMALIZED_EXPRESSION&$format=xml',
'subs': ['bto', 'swissprot_only', 'isoform']
},
'abs': {
'label': '',
'url': 'http://genome.crg.es/datasets/abs2005/data/abs.gff'
},
'uniprot_sec': {
'label': 'Secondary UniProt ACs',
'url_old': 'ftp://ftp.uniprot.org/pub/databases/uniprot/'
'current_release/knowledgebase/complete/docs/sec_ac.txt',
'url': 'ftp://ftp.expasy.org/databases/uniprot/current_release/'
'knowledgebase/complete/docs/sec_ac.txt',
},
'uniprot_idmap_ftp': {
'label': 'Human ID mapping from UniProt',
'url': 'ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/'
'knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz'
},
'uniprot_idmap': {
'label': 'ID mapping from UniProt',
'url': 'http://uniprot.org/mapping/'
},
'pazar': {
'label': 'TF-target gene lists from PAZAR',
'url': 'http://www.pazar.info/tftargets/tftargets.zip',
'url_rescued': 'http://rescued.omnipathdb.org/pazar_tftargets.zip',
},
'htri': {
'label': 'TF-target gene lists from HTRI',
'url': 'https://rescued.omnipathdb.org/HTRIdb.csv',
'url_old1': 'http://www.lbbc.ibb.unesp.br/htri/datasHTRIdb?down=3',
'url_old2': 'http://www.lbbc.ibb.unesp.br/htri/consulta?'\
'type=1&all=true&down=3&iconss1.x=57&iconss1.y=48',
'init_url': 'http://www.lbbc.ibb.unesp.br/htri/consulta?'\
'type=1&all=true&down=3',
},
'oreganno_old': {
'label': 'TF-target gene lists from ORegAnno, previous version',
'url': 'http://www.oreganno.org/oregano/htdocs'
'/data/oreganno_UCSC_08Nov10.txt.gz'
},
'oreganno': {
'label': 'TF-target gene lists from ORegAnno',
'url_old': 'http://py-gi1.stanford.edu:8080/oregano/htdocs/'
'downloads/ORegAnno_Combined_2015.09.16.tsv',
'url': 'http://www.oreganno.org/dump/'\
'ORegAnno_Combined_2016.01.19.tsv',
},
'cpdb': {
'label': 'All human interactions from ConsensusPathDB',
'url':
'http://cpdb.molgen.mpg.de/download/ConsensusPathDB_human_PPI.gz'
},
'goa': {
'label': 'UniProt GO annotations from GOA',
'go_url': 'http://geneontology.org/gene-associations/goa_%s.gaf.gz',
'ebi_url_old': 'ftp://ftp.ebi.ac.uk/pub/'
'databases/GO/goa/%s/goa_%s.gaf.gz',
'ebi_url': 'https://ftp.ebi.ac.uk/pub/databases/GO/'
'goa/%s/goa_%s.gaf.gz',
},
'quickgo_old': {
'label': 'UniProt GO annotations from QuickGO',
'url': 'http://www.ebi.ac.uk/QuickGO/GAnnotation?format=tsv&'
'limit=-1%s&termUse=%s&tax=%u&col=proteinID,goID,goName,aspect'
},
'quickgo': {
'label': 'UniProt GO annotations from QuickGO',
'url': 'https://www.ebi.ac.uk/QuickGO/services/annotation/'\
'downloadSearch?includeFields=goName,name&taxonId=%u'
'&aspect=%s%s'
},
'quickgo_rest': {
'label': 'REST API of the QuickGO Gene Ontology server',
'graph': 'https://www.ebi.ac.uk/QuickGO/services/ontology/'\
'go/terms/graph?startIds=%s,relations=%s',
'terms': 'https://www.ebi.ac.uk/QuickGO/services/ontology/'\
'go/terms?page=%u',
'annot': 'https://www.ebi.ac.uk/QuickGO/services/annotation/'\
'downloadSearch?'\
'includeFields=goName&'\
'includeFields=taxonName&'\
'includeFields=name&'\
'aspect=%s&'\
'goUsageRelationships=%s&'\
'taxonId=%u&'\
'limit=100&'\
'page=%u',
'desc': 'https://www.ebi.ac.uk/QuickGO/services/ontology/'\
'go/terms/%s/descendants%s',
},
'quickgo_desc': {
'label': 'UniProt GO annotations from QuickGO',
'url': 'https://www.ebi.ac.uk/QuickGO/services/annotation/'\
'downloadSearch?includeFields=goName,name&taxonId=%u'\
'&goUsage=descendants&goId=%s'
},
'goose': {
'label': 'Legacy MySQL query interface of AmiGO',
'url': 'http://amigo.geneontology.org/goose?query=%s'\
'&mirror=bbop&limit=0&format=text',
},
'golr': {
'label': 'AmiGO Solr service URL',
'url': 'http://golr.berkeleybop.org/select%s'
},
'goslim_gen': {
'label': 'Generic GOSlim from GO Consortium',
'url':
'http://www.geneontology.org/ontology/subsets/goslim_generic.obo'
},
'go': {
'label': 'The whole Gene Ontology',
'url': 'http://purl.obolibrary.org/obo/go.obo'
},
'netpath_names': {
'label': 'NetPath numeric pathway IDs can be translated to '
'pathway names only by extracting them from HTML....',
'url': 'http://www.netpath.org/browse'
},
'netpath_pw': {
'label': 'NetPath pathway page',
'mainpage': 'http://mirror.netpath.org/index.html',
'url': 'http://mirror.netpath.org/pathways?path_id=NetPath_%u'
},
'netpath_psimi': {
'label': 'Batch download of NetPath pathways in PSI-MI format',
'url': 'http://rescued.omnipathdb.org/NetPath_PSI-MI.zip'
},
'netpath_bp': {
'label': 'Netpath pathways one by one in BioPAX level 3 format',
'biopax_l3': 'http://www.netpath.org/data/biopax/NetPath_%u.owl'
},
'proteomemap': {
'label':
'Human Proteome Map: Mass-spec expression data in '\
'healthy human tissues',
'url':
'http://www.humanproteomemap.org/Download_HPM/HPM_protein_level_'
'expression_matrix_Kim_et_al_052914.csv'
},
'proteinatlas': {
'label': 'Human Protein Atlas: Immuncytochemistry expression data in '
'healthy human cells or cancer cells or cell lines',
'normal': 'http://www.proteinatlas.org/download/'\
'normal_tissue.tsv.zip',
'pathology': 'http://www.proteinatlas.org/download/pathology.tsv.zip',
'subcell': 'https://www.proteinatlas.org/download/'\
'subcellular_location.tsv.zip',
'secretome_old': 'https://stke.sciencemag.org/highwire/filestream/'\
'216463/field_highwire_adjunct_files/1/aaz0274_Data_file_S2.xlsx',
'secretome': 'https://www.science.org/action/downloadSupplement?'\
'doi=10.1126%2Fscisignal.aaz0274&'\
'file=aaz0274_data_file_s2.xlsx',
'ig_genes': 'https://stke.sciencemag.org/highwire/filestream/'\
'216463/field_highwire_adjunct_files/0/aaz0274_Data_file_S1.xlsx',
},
'lincs-compounds': {
'label':
'List of small molecules in LINCS with synonyms and PubChem IDs',
'url': 'http://lincs.hms.harvard.edu/db/datasets/20000/smallmolecules'
'?search=&output_type=.csv'
},
'eutils': {
'label': 'NCBI E-Utils API',
'esummary': 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi',
'pmc-idconv': (
'https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/'
'v1.0/?ids=%s&format=json'
),
},
'pubmed': {
'label': 'PubMed baseurl',
'url': 'http://www.ncbi.nlm.nih.gov/pubmed/%s'
},
'hpmr': {
'label': 'Human Plasma Membrane Receptome',
'url':
'http://www.receptome.org/SearchDB/findGenes.asp?textName='
},
'tfcensus': {
'label': 'A census of human transcription factors (Vaquerizas 2009)',
'url': (
r'https://static-content.springer.com/esm/'
r'art%3A10.1038%2Fnrg2538/MediaObjects/'
r'41576_2009_BFnrg2538_MOESM6_ESM.txt'
)
},
'tfcheckp': {
'label': 'A comprehensive list of transcription factors',
'url':
'http://www.tfcheckpoint.org/data/TFCheckpoint_download_180515.txt'
},
'gtp': {
'label': 'Guide to Pharmacology: ligand-receptor interactions',
'url': 'http://www.guidetopharmacology.org/DATA/interactions.csv',
},
'giant': {
'label': 'JSON network from GIANT by gene based query',
'init_url': 'http://giant.princeton.edu/',
'url':
'http://giant.princeton.edu/contexts/integration/'\
'query/%u/?%s&prior=0.1'
},
'msigdb': {
'label': 'Molecular Signatures Database',
'login1': 'https://www.gsea-msigdb.org/gsea/login',
'login2': 'https://www.gsea-msigdb.org/gsea/j_spring_security_check',
'url': 'https://www.gsea-msigdb.org/gsea/msigdb/'
'download_file.jsp?filePath=/msigdb/release/'
'%s.%s/%s.v%s.%s.%s.gmt',
'coll': 'https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp',
'url_stem': 'https://www.gsea-msigdb.org/gsea/%s',
'one_set': 'hhttps://www.gsea-msigdb.org/gsea/msigdb/'
'download_geneset.jsp?geneSetName=%s&fileType=txt',
'url_all': 'https://www.gsea-msigdb.org/gsea/msigdb/'\
'download_file.jsp?filePath=/msigdb/release/7.5.1/'\
'msigdb_v7.5.1_files_to_download_locally.zip',
},
'msigdb_old': {
'label': 'Molecular Signatures Database',
'login1': 'http://software.broadinstitute.org/gsea/login.jsp',
'login2':
'http://software.broadinstitute.org/gsea/j_spring_security_check',
'url': 'http://software.broadinstitute.org/gsea/msigdb/'
'download_file.jsp?filePath=/resources/msigdb/7.0/%s.v7.0.%s.gmt',
'coll': 'http://www.broadinstitute.org/gsea/msigdb/collections.jsp',
'url_stem': 'http://www.broadinstitute.org/gsea/%s',
'one_set':
'http://www.broadinstitute.org/gsea/msigdb/download_geneset.jsp?'
'geneSetName=%s&fileType=txt',
'url_all': 'http://software.broadinstitute.org/gsea/msigdb/'\
'download_file.jsp?filePath=/resources/msigdb/7.0/'\
'msigdb_v7.0_files_to_download_locally.zip',
},
'disgenet': {
'api_url': 'https://www.disgenet.org/api',
'disease_id_mappings': 'https://www.disgenet.org/static/disgenet_ap1/files/downloads/disease_mappings.tsv.gz',
'variant_gene_mappings': 'https://www.disgenet.org/static/disgenet_ap1/files/downloads/variant_to_gene_mappings.tsv.gz',
'annotation_label': 'Disease-gene associations',
'annotations': 'http://www.disgenet.org/static/disgenet_ap1/files/'\
'downloads/%s_gene_disease_associations.tsv.gz',
'annotation_datasets': ['curated', 'literature', 'befree', 'all'],
},
'hsn': {
'label': 'The Wang Human Signaling Network',
'rescued': (
'http://rescued.omnipathdb.org/WangLab_HumanSignalingNet_v6.csv'
),
'researchgate': 'https://www.researchgate.net/profile/Edwin-Wang-6/'
'publication/264488606_Human_Signaling_Network_Version_6/data/'
'53e102ed0cf2235f35271ea3/'
'HuamnSignalingNet-v6.csv?origin=publication_detail',
},
'li2012': {
'label': 'Human Phosphotyrosine Signaling Network',
'url': 'http://genome.cshlp.org/content/suppl/2011/12/27/'
'gr.128819.111.DC1/Supplementary_files_S1-S5.xls'
},
'trip': {
'label': 'The TRP channel database',
'base': 'http://www.trpchannel.org/',
'base_rescued': 'https://rescued.omnipathdb.org/trip/main.html',
'show': 'http://www.trpchannel.org/proteins/show?id=%s',
'show_rescued': 'https://rescued.omnipathdb.org/trip/show-%s.html',
'intr': 'http://www.trpchannel.org/interactions/show?trp=%s&'
'interactor=%s',
'url': 'http://www.trpchannel.org/20141116.csv',
'json': 'http://www.trpchannel.org/proteins/getjson'
},
'signor': {
'label': 'SIGNOR pathways',
'list_url': 'https://signor.uniroma2.it/downloads.php',
'base_url': 'https://signor.uniroma2.it/%s',
'all_url': 'https://signor.uniroma2.it/DownloadServlet?action=all',
'all_url_new': 'https://signor.uniroma2.it/download_entity.php',
'complexes': 'https://signor.uniroma2.it/download_complexes.php',
},
'hiii14': {
'label': 'Rolland et al 2014, Human Interactome II',
'url':
'http://www.cell.com/cms/attachment/2021150198/2041343422/mmc3.xlsx',
'article_url': 'https://www.cell.com/cell/fulltext/'
'S0092-8674(14)01422-6',
},
'kinome': {
'label': 'List of human kinases',
'url': 'http://kinase.com/static/colt/data/human/kinome/tables/'
'Kincat_Hsap.08.02.xls',
'rescued': 'https://rescued.omnipathdb.org/Kincat_Hsap.08.02.xls',
},
'phosphatome': {
'label': 'List of human and other phosphatases',
'webpage': 'http://phosphatome.net/3.0',
'url_from_page': 'https://www.science.org/doi/suppl/10.1126/'\
'scisignal.aag1796/suppl_file/aag1796_tables_s1_to_s23.zip',
'url': 'https://www.science.org/action/downloadSupplement?'
'doi=10.1126%2Fscisignal.aag1796&'
'file=aag1796_tables_s1_to_s23.zip',
},
'dgidb': {
'label': 'Druggable genes compiled from multiple resources',
'main_url': 'http://dgidb.genome.wustl.edu/search_categories',
'url': 'http://dgidb.genome.wustl.edu/druggable_gene_categories/%s?'
'sources=BaderLabGenes,CarisMolecularIntelligence,'
'FoundationOneGenes,GO,GuideToPharmacologyGenes,HopkinsGroom,'
'MskImpact,RussLampel,dGene',
'categories': 'https://www.dgidb.org/data/monthly_tsvs/'
'2021-Jan/categories.tsv',
'interactions': 'https://www.dgidb.org/data/monthly_tsvs/'
'2022-Feb/interactions.tsv',
},
'reactome': {
'label': 'The Reactome reaction network database',
'sbml':
'https://reactome.org/download/current/homo_sapiens.3.1.sbml.tgz',
'biopax_l3': 'https://reactome.org/download/current/biopax.zip',
'biopax_l2': 'https://reactome.org/download/current/biopax2.zip',
},
'acsn': {
'label': 'Atlas of Cancer Signaling Networks',
'biopax_l3': 'https://acsn.curie.fr/files/acsn_v1.1.owl',
'sif': 'https://acsn.curie.fr/files/acsn_ppi.sif',
'ppi': 'http://rescued.omnipathdb.org/acsn_ppi.txt',
'names': 'http://rescued.omnipathdb.org/acsn_names.gmt',
},
'nci-pid': {
'label': 'National Cancer Institute -- Pathway Interaction Database',
'biopax_l3':
'ftp://ftp1.nci.nih.gov/pub/PID/BioPAX_Level_3/'\
'NCI-Nature_Curated.bp3.owl.gz'
},
'panther': {
'label': 'PANTHER pathways',
'biopax_l3':
'ftp://ftp.pantherdb.org//pathway/current_release/BioPAX.tar.gz'
},
'laudanna': {
'label':
'Directionality and effect information inferred from multiple'\
' sources by Laudanna Lab',
'sigflow':
'http://dp.univr.it/~laudanna/LCTST/downloads/files/SignalingFlow.EA',
'sigdir':
'http://dp.univr.it/~laudanna/LCTST/downloads/files/'\
'SignalingDirection.EA',
'sigdir_rescued': 'https://rescued.omnipathdb.org/'\
'Laudanna_SignalingDirection.EA',
'sigflow_rescued': 'https://rescued.omnipathdb.org/'\
'Laudanna_SignalingFlow.EA',
},
'biogrid': {
'label': 'BioGRID version 2 tab format',
'mv': 'https://downloads.thebiogrid.org/Download/BioGRID/Latest-Release/'\
'BIOGRID-MV-Physical-LATEST.tab2.zip',
'all': 'https://downloads.thebiogrid.org/Download/BioGRID/Latest-Release/'\
'BIOGRID-ALL-LATEST.tab2.zip'
},
'wang': {
'label':
'Human Signaling Network compiled by Wang Group, version 6 (2014)',
'old_url': 'http://www.bri.nrc.ca/wang/cancerMap/'
'HumanSignalingNetwork_v6.csv',
'rescued': 'https://rescued.omnipathdb.org/'
'WangLab_HumanSignalingNetwork_v6-format2.csv',
'cui': 'https://www.embopress.org/action/downloadSupplement?'
'doi=10.1038%2Fmsb4100200&file=msb4100200-sup-0010.xls',
'cui_init': 'https://www.embopress.org/doi/full/10.1038/msb4100200',
},
'graphviz': {
'label': 'List of Graphviz attributes',
'url': 'http://www.graphviz.org/doc/info/attrs.html'
},
'hid': {
'label': 'CCSB Human Interactome Project',
'lit-bm-13': 'http://interactome.dfci.harvard.edu/H_sapiens/'
'download/Lit-BM-13.tsv',
'hi-ii-14':
'http://interactome.dfci.harvard.edu/H_sapiens/download/HI-II-14.psi',
'hi-i-05':
'http://interactome.dfci.harvard.edu/H_sapiens/download/HI-I-05.psi',
'lit-bm-17': 'https://rescued.omnipathdb.org/LitBM-17.psi',
'lit-bm': 'http://www.interactome-atlas.org/data/Lit-BM.tsv',
'huri': 'http://www.interactome-atlas.org/data/HuRI.psi',
'hi-union': 'http://www.interactome-atlas.org/data/HI-union.psi',
'yang-2016': 'http://www.interactome-atlas.org/data/Yang-16.psi',
'hi-i-05-pmi': 'http://www.interactome-atlas.org/data/H-I-05.psi',
'hi-ii-14-pmi': 'http://www.interactome-atlas.org/data/HI-II-14.psi',
'yu-2011': 'http://www.interactome-atlas.org/data/Yu-11.psi',
},
'ca1': {
'label': 'Supplementary Online Materials for Ma\'ayan 2005',
'url_old': 'http://science.sciencemag.org/highwire/filestream/586741/'
'field_highwire_adjunct_files/1/Maayan_SOM_External_Files.zip',
'url': 'https://www.science.org/action/downloadSupplement?'
'doi=10.1126%2Fscience.1108876&'
'file=maayan_som_external_files.zip',
},
'ccmap': {
'label': 'Cancer Cell Map from PathwayCommons 2011 snapshot',
'edges':
'http://www.pathwaycommons.org/archives/PC1/last_release-2011/'\
'tab_delim_network/by_source/cell-map-edge-attributes.txt.zip',
'nodes':
'http://www.pathwaycommons.org/archives/PC1/last_release-2011/'\
'tab_delim_network/by_source/cell-map-node-attributes.txt.zip'
},
'pathguide': {
'label':
'Collection of metabolic and signaling pathway and molecular '\
'interaction resources',
'url':
'http://pathguide.org/fullrecord.php?organisms=all&'\
'availability=all&standards=all&order=alphabetic&DBID=%u'
},
'cgc': {
'label': 'Cancer Gene Census: list of cancer related (driver) genes',
'host': 'sftp-cancer.sanger.ac.uk',
'file': '/files/grch38/cosmic/v76/cancer_gene_census.csv',
'url_new': 'https://cancer.sanger.ac.uk/cosmic/file_download/'
'GRCh38/cosmic/v94/cancer_gene_census.csv',
},
'havugimana': {
'label': 'Census of human soluble protein complexes',
'url': 'https://www.cell.com/cms/10.1016/j.cell.2012.08.011/'
'attachment/852fdb4f-ef77-4001-b513-a6687e6e070f/mmc3.xls',
'article': 'https://www.cell.com/fulltext/S0092-8674(12)01006-9',
},
'matrixdb': {
'label': 'MatrixDB in house curated interactions, PSI-MI tab format',
'old_url': 'http://matrixdb.ibcp.fr/download/matrixdb_CORE.tab.gz',
'url': 'http://matrixdb.univ-lyon1.fr/download/matrixdb_CORE.tab.gz',
'ecm_proteins': 'http://matrixdb.univ-lyon1.fr/'\
'download//proteins_ECM.csv',
'secreted_proteins': 'http://matrixdb.univ-lyon1.fr/'
'download//proteins_Secreted.csv',
'membrane_proteins': 'http://matrixdb.univ-lyon1.fr/'
'download//proteins_Membrane.csv',
},
'innatedb': {
'label': 'InnateDB PSI-MI tab',
'url':
'http://innatedb.com/download/interactions/innatedb_ppi.mitab.gz'
},
'dip': {
'label': 'DIP PSI-MI tab',
'login': 'http://dip.doe-mbi.ucla.edu/dip/Login.cgi',
'url_old': 'http://dip.mbi.ucla.edu/dip/file?'
'ds=current&fn=Hsapi20170205%s&ff=txt',
'ik': 'http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?IK=%u',
'url': 'https://dip.doe-mbi.ucla.edu/dip/File.cgi?FN=2017/tab25/'
'Hsapi20170205.txt.gz',
'url_rescued': 'https://rescued.omnipathdb.org/dip/'
'Hsapi20170205%s.txt.gz',
},
'vaquerizas2009': {
'label': 'A census of human transcription factors: function, '
'expression and evolution; Supplementary Table S3',
'url': (
r'https://static-content.springer.com/esm/'
r'art%3A10.1038%2Fnrg2538/MediaObjects/'
r'41576_2009_BFnrg2538_MOESM6_ESM.txt'
),
},
'spike': {
'label': 'SPIKE database XML',
'url': 'http://www.cs.tau.ac.il/~spike/download/LatestSpikeDB.xml.zip'
},
'mppi': {
'label': 'MIPS PPI full download',
'url': 'http://mips.helmholtz-muenchen.de/proj/ppi/data/mppi.gz',
'url_rescued': 'https://rescued.omnipathdb.org/mppi.gz',
},
'negatome': {
'label': 'Negatome manually curated non-interacting protein pairs',
'manual':
'http://mips.helmholtz-muenchen.de/proj/ppi/negatome/manual.txt'
},
'macrophage': {
'label': 'Macrophage Pathways; Raza 2010, Supplementary Materials 1',
'url': r'https://static-content.springer.com/esm/art%3A10.1186%2F1752-'
r'0509-4-63/MediaObjects/12918_2010_452_MOESM2_ESM.XLS'
},
'intact': {
'label': 'IntAct entire database PSI-MI tab',
'mitab': 'https://ftp.ebi.ac.uk/pub/databases/intact/'
'current/psimitab/intact.zip'
},
'death': {
'label': 'DeathDomain webpage',
'url_dead': 'http://www.deathdomain.org/proteins/show?family=%s',
'url_alive': 'http://rescued.omnipathdb.org/deathdomain.tsv',
},
'string': {
'label': 'STRING',
'actions': 'https://stringdb-downloads.org/download/'
'protein.actions.v12.0/%u.protein.actions.v12.0.txt.gz',
'links': 'https://stringdb-downloads.org/download/protein.links.detailed.v12.0/%u'
'.protein.links.detailed.v12.0.txt.gz',
'physical_links': 'https://stringdb-downloads.org/download/protein.physical.links.detailed.v12.0/%u'
'.protein.physical.links.detailed.v12.0.txt.gz',
'species': 'https://stringdb-downloads.org/download/species.v12.0.txt'
},
'wikipw': {
'label': 'WikiPathways human biopax',
'biopax_l3_old': 'http://wikipathways.org//wpi/cache/wikipathways_'
'Homo_sapiens_Curation-AnalysisCollection__owl.zip',
'biopax_l3': 'http://data.wikipathways.org/20191010/gpml/'
'wikipathways-20191010-gpml-Homo_sapiens.zip',
},
'pwcommons': {
'label': 'PathwayCommons binary SIF files',
'url': 'https://www.pathwaycommons.org/archives/PC2/v%u/'
'PathwayCommons%u.%s.hgnc.sif.gz',
},
'homologene': {
'label': 'NCBI HomoloGene data, recent release',
'url': 'https://ftp.ncbi.nih.gov/pub/HomoloGene/'
'current/homologene.data',
},
'mirbase' : {
'label': 'miRBase: miRNA main reference database',
'aliases_old': 'ftp://mirbase.org/pub/mirbase/CURRENT/aliases.txt.gz',
'aliases': 'https://mirbase.org/ftp/CURRENT/aliases.txt.gz',
},
'mir2dis': {
'label': 'miR2Disease experimentally validated'\
'miRNA-target interactions',
'url': 'http://watson.compbio.iupui.edu:8080'\
'/miR2Disease/download/miRtar.txt',
'url_rescued': 'http://rescued.omnipathdb.org/miR2Disease_miRtar.txt',
},
'mirdeathdb': {
'label': 'miRDeathDB experimentally verified'\