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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

adeptus icon adeptus

Convert differential gene expression signatures for diseases from ADEPTUS to BEL

bio2bel icon bio2bel

A Python framework for integrating biological databases and structured data sources in Biological Expression Language (BEL)

bio2bel-manuscript icon bio2bel-manuscript

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

bkms icon bkms

A Bio2BEL package for converting BMKS-react to BEL

chebi icon chebi

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

chembl icon chembl

A Bio2BEL package for converting biochemical inhibition and binding information in ChEMBL to BEL

cmo icon cmo

Convert the Clinical Measurement Ontology to BEL

creeds icon creeds

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

ctd icon ctd

A Bio2BEL package for converting the Comparative Toxicogenomics Database (CTD) to BEL

dbsnp icon dbsnp

Converting dbSNP mutation information to BEL

ddr icon ddr

Disease-disease relationships from Menche et al.

doid icon doid

A Bio2BEL package for the Disease Ontology (http://www.disease-ontology.org)

drugbank icon drugbank

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

efo icon efo

Experimental Factor Ontology (EFO) to BEL

entrez icon entrez

A Bio2BEL package for converting Entrez and HomoloGene to BEL

excape icon excape

Convert curated assays from ExCAPE-DB to BEL

expasy icon expasy

A Bio2BEL package for converting ExPASy to BEL

flybase icon flybase

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

gfam icon gfam

[DEPRECATED] HGNC Gene Families to BEL

go icon go

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

hgnc icon hgnc

Hugo Gene Nomenclature Consortium (HGNC) to BEL

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