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Bio2BEL is a project aimed at bringing biological databases and other structured knowledge sources in a wide variety of schemata into the unified framework of the Biological Expression Language [1].

Two important places to look:

Installation Current version on PyPI Stable Supported Python Versions MIT License

Download the latest stable code from PyPI with:

$ python -m pip install bio2bel

or get the latest from GitHub with:

$ git clone https://github.com/bio2bel/bio2bel.git
$ cd bio2bel
$ python -m pip install -e .

or check the installation instructions.

Citation

If you find Bio2BEL useful for your work, please consider citing:

[1]Hoyt, C. T., et al. (2019). Integration of Structured Biological Data Sources using Biological Expression Language. bioRxiv, 631812.

Bio2BEL's Projects

hmdb icon hmdb

A Bio2BEL package for converting the Human Metabolite Database (HMDB) to BEL

hmdd icon hmdd

A Bio2BEL package for converting the Human microRNA Disease Database (HMDD) to BEL

hp icon hp

A Bio2BEL package for converting the Human Phenotype Ontology (HP) to BEL

hsdn icon hsdn

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

interpro icon interpro

A Bio2BEL package for converting InterPro to BEL

kegg icon kegg

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

mesh icon mesh

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

mgi icon mgi

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

mir2disease icon mir2disease

A Bio2BEL package for mir2disease (http://www.mir2disease.org)

mirbase icon mirbase

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

mirtarbase icon mirtarbase

Serializes text-mined miRNA-target interactions to BEL

msig icon msig

Integration of pathway-related information from MSigDB in BEL

pfam icon pfam

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

reactome icon reactome

Integration of pathway-related information from Reactome in BEL

regnetwork icon regnetwork

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

rgd icon rgd

Rat Genome Database to BEL

sider icon sider

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

uberon icon uberon

Uber Anatomy Ontology (UBERON) to BEL

wikipathways icon wikipathways

Integration of pathway-related information from WikiPathways in BEL

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