Bio2BEL

bio2bel

A Python framework for integrating biological databases and structured data sources in BEL

data-integration ontologies biological-expression-language

Python Apache-2.0 0 3 14 0 Updated Nov 15, 2019

flybase

A Bio2BEL package for the terminology from FlyBase (http://flybase.org/)

systems-biology genes drosophila terminology biological-expression-language networks-biology orthology

Python MIT 0 0 0 0 Updated Nov 13, 2019

hsdn

Convert Himmerlstein's reproduction of the Human Symptom-Disease network to BEL

disease symptoms biological-expression-language disease-symptom

Python MIT 0 0 0 0 Updated Nov 13, 2019

pfam

A Bio2BEL package for PFAM (https://pfam.xfam.org/)

terminology biological-expression-language pfam protein-families

Python MIT 0 0 0 0 Updated Nov 13, 2019

phosphosite

biological-expression-language protein-modifications post-translational-modification

Python MIT 0 0 1 0 Updated Nov 13, 2019

regnetwork

A Bio2BEL package for RegNetwork (http://www.regnetworkweb.org)

Python MIT 0 0 0 0 Updated Nov 13, 2019

phewascatalog

Python MIT 0 0 1 0 Updated Nov 13, 2019

mgi

A Bio2BEL package for converting the Mouse Genome Informatics Database (MGI) to BEL

genes terminology biological-expression-language orthology mgi

Python MIT 0 0 0 0 Updated Nov 13, 2019

mirbase

A Bio2BEL package for miRBase (http://www.mirbase.org)

biological-expression-language mirna microrna mirbase

Python MIT 0 0 3 0 Updated Nov 13, 2019

chebi

A Bio2BEL package for converting Chemical Entities of Biological Interest (ChEBI) to BEL

chemistry terminology chemoinformatics biological-expression-language chebi

Python MIT 1 0 4 0 Updated Nov 13, 2019

dbsnp

Converting dbSNP mutation information to BEL

Python MIT 0 0 1 0 Updated Nov 11, 2019

sider

A Bio2BEL package for the Side Effect Resource (SIDER; http://sideeffects.embl.de/)

chemistry sider biological-expression-language side-effects

Jupyter Notebook MIT 1 0 0 0 Updated Oct 24, 2019

drugbank

A Bio2BEL package for DrugBank (https://www.drugbank.ca)

cheminformatics pharmacology systems-biology drugbank drugs terminology biological-expression-language

Python MIT 3 1 3 0 Updated Oct 15, 2019

hgnc

Hugo Gene Nomenclature Consortium (HGNC) to BEL

hgnc genes terminology biological-expression-language

Python MIT 0 0 1 0 Updated Sep 26, 2019

entrez

A Bio2BEL package for converting Entrez and HomoloGene to BEL

bioinformatics systems-biology genes terminology entrez-gene biological-expression-language networks-biology

Python MIT 0 0 1 0 Updated Sep 26, 2019

creeds

Public differential gene expression profiles from http://amp.pharm.mssm.edu/CREEDS/

Jupyter Notebook MIT 0 0 0 0 Updated Sep 22, 2019

bio2bel-cookiecutter

A cookiecutter bio2bel repositories

Python MIT 1 0 0 0 Updated Sep 22, 2019

rgd

Rat Genome Database to BEL

genes terminology biological-expression-language rgd

Python MIT 0 0 0 0 Updated Sep 22, 2019

bio2bel-manuscript

LaTeX source for "Bio2BEL: Integration of Structured Knowledge with Biological Expression Language"

systems-biology semantic-web biological-expression-language networks-biology

TeX 0 0 1 0 Updated Sep 17, 2019

go

A Bio2BEL package for converting the Gene Ontology (GO) to BEL

systems-biology ontology gene-ontology terminology pathways biological-expression-language networks-biology

Python MIT 0 0 1 0 Updated Sep 6, 2019

hippie

Convert PPIs in HIPPIE to BEL

biological-expression-language protein-protein-interactions

Python MIT 0 0 0 0 Updated Aug 26, 2019

uniprot

UniProt Knowledge Base to BEL

proteins terminology uniprot biological-expression-language

Python MIT 1 0 3 0 Updated Aug 21, 2019

expasy

A Bio2BEL package for converting ExPASy to BEL

proteins systems-biology biological-expression-language protein-families networks-biology expasy

Python MIT 0 0 1 0 Updated Aug 19, 2019

gwascatalog

Python MIT 0 0 0 0 Updated Aug 13, 2019

famplex

Convert FamPlex to BEL

ontology terminology biological-expression-language protein-families protein-complexes

Python MIT 0 0 0 0 Updated Aug 13, 2019

adeptus

Convert differential gene expression signatures for diseases from ADEPTUS to BEL

gene-expression biological-expression-language differential-gene-expression pathology

Python MIT 0 0 0 0 Updated Aug 13, 2019

bio2bel-notebooks

Notebooks demonstrating the usage of Bio2BEL packages

semantics jupyter-notebook data-integration biological-expression-language

Jupyter Notebook Apache-2.0 1 0 1 0 Updated Aug 12, 2019

wikipathways

Integration of pathway-related information from WikiPathways in BEL

systems-biology pathways wikipathways biological-expression-language

Python MIT 1 1 0 0 Updated Aug 6, 2019

mesh

A Bio2BEL package for the Medical Subject Headings (MeSH; https://meshb.nlm.nih.gov)

chemistry mesh terminology phenotypes biological-expression-language

Python MIT 0 0 2 0 Updated Aug 2, 2019

kegg

A Bio2BEL package for integrating pathway-related information from KEGG in BEL

proteins systems-biology pathways kegg biological-expression-language networks-biology

Python MIT 1 3 1 0 Updated Jul 1, 2019

Bio2BEL

bio2bel

flybase

hsdn

pfam

phosphosite

regnetwork

phewascatalog

mgi

mirbase

chebi

dbsnp

sider

drugbank

hgnc

entrez

creeds

bio2bel-cookiecutter

rgd

bio2bel-manuscript

go

hippie

uniprot

expasy

gwascatalog

famplex

adeptus

bio2bel-notebooks

wikipathways

mesh

kegg

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