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Access to Biological Web Services from Python

Project description

https://badge.fury.io/py/bioservices.svg https://github.com/cokelaer/bioservices/actions/workflows/ci.yml/badge.svg Documentation Status https://raw.githubusercontent.com/cokelaer/bioservices/master/doc/bioservices.png
Python_version_available:

BioServices is tested for Python 3.6, 3.7, 3.8

Contributions:

Please join https://github.com/cokelaer/bioservices and share your notebooks https://github.com/bioservices/notebooks/

Issues:

Please use https://github.com/cokelaer/bioservices/issues

How to cite:

Cokelaer et al. BioServices: a common Python package to access biological Web Services programmatically Bioinformatics (2013) 29 (24): 3241-3242

Documentation:

RTD documentation.

Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols).

The primary goal of BioServices is to use Python as a glue language to provide a programmatic access to several Bioinformatics Web Services. By doing so, elaboration of new applications that combine several of the wrapped Web Services is fostered.

One of the main philosophy of BioServices is to make use of the existing biological databases (not to re-invent new databases) and to alleviates the needs for expertise in Web Services for the developers/users.

BioServices provides access to about 40 Web Services.

Here is a small example using the UniProt Web Service to search for the zap70 specy in human organism:

>>> from bioservices import UniProt
>>> u = UniProt(verbose=False)
>>> data = u.search("zap70+and+taxonomy:9606", frmt="tab", limit=3,
...                 columns="entry name,length,id, genes")
>>> print(data)
Entry name   Length  Entry   Gene names
ZAP70_HUMAN  619     P43403  ZAP70 SRK
B4E0E2_HUMAN 185     B4E0E2
RHOH_HUMAN   191     Q15669  RHOH ARHH TTF

More examples and tutorials are available in the On-line documentation

Here is the list of services available and their testing status.

Service

CI testing

arrayexpress

https://github.com/cokelaer/bioservices/actions/workflows/arrayexpress.yml/badge.svg

bigg

https://github.com/cokelaer/bioservices/actions/workflows/bigg.yml/badge.svg

biocarta

https://github.com/cokelaer/bioservices/actions/workflows/biocarta.yml/badge.svg

biodbnet

https://github.com/cokelaer/bioservices/actions/workflows/biodbnet.yml/badge.svg

biogrid

https://github.com/cokelaer/bioservices/actions/workflows/biogrid.yml/badge.svg

biomart

https://github.com/cokelaer/bioservices/actions/workflows/biomart.yml/badge.svg

biomodels

https://github.com/cokelaer/bioservices/actions/workflows/biomodels.yml/badge.svg

chebi

https://github.com/cokelaer/bioservices/actions/workflows/chebi.yml/badge.svg

chembl

https://github.com/cokelaer/bioservices/actions/workflows/chembl.yml/badge.svg

cog

https://github.com/cokelaer/bioservices/actions/workflows/cog.yml/badge.svg

dbfetch

https://github.com/cokelaer/bioservices/actions/workflows/dbfetch.yml/badge.svg

ena

https://github.com/cokelaer/bioservices/actions/workflows/ena.yml/badge.svg

ensembl

https://github.com/cokelaer/bioservices/actions/workflows/ensembl.yml/badge.svg

eutils

https://github.com/cokelaer/bioservices/actions/workflows/eutils.yml/badge.svg

eva

https://github.com/cokelaer/bioservices/actions/workflows/eva.yml/badge.svg

hgnc

https://github.com/cokelaer/bioservices/actions/workflows/hgnc.yml/badge.svg

intact_complex

https://github.com/cokelaer/bioservices/actions/workflows/intact_complex.yml/badge.svg

kegg

https://github.com/cokelaer/bioservices/actions/workflows/kegg.yml/badge.svg

muscle

https://github.com/cokelaer/bioservices/actions/workflows/muscle.yml/badge.svg

mygeneinfo

https://github.com/cokelaer/bioservices/actions/workflows/mygeneinfo.yml/badge.svg

ncbiblast

https://github.com/cokelaer/bioservices/actions/workflows/ncbiblast.yml/badge.svg

omicsdi

https://github.com/cokelaer/bioservices/actions/workflows/omicsdi.yml/badge.svg

omnipath

https://github.com/cokelaer/bioservices/actions/workflows/omnipath.yml/badge.svg

panther

https://github.com/cokelaer/bioservices/actions/workflows/panther.yml/badge.svg

pathwaycommons

https://github.com/cokelaer/bioservices/actions/workflows/pathwaycommons.yml/badge.svg

pdb

https://github.com/cokelaer/bioservices/actions/workflows/pdb.yml/badge.svg

pdbe

https://github.com/cokelaer/bioservices/actions/workflows/pdbe.yml/badge.svg

pfam

https://github.com/cokelaer/bioservices/actions/workflows/pfam.yml/badge.svg

pride

https://github.com/cokelaer/bioservices/actions/workflows/pride.yml/badge.svg

psicquic

https://github.com/cokelaer/bioservices/actions/workflows/psicquic.yml/badge.svg

pubchem

https://github.com/cokelaer/bioservices/actions/workflows/pubchem.yml/badge.svg

quickgo

https://github.com/cokelaer/bioservices/actions/workflows/quickgo.yml/badge.svg

reactome

https://github.com/cokelaer/bioservices/actions/workflows/reactome.yml/badge.svg

rhea

https://github.com/cokelaer/bioservices/actions/workflows/rhea.yml/badge.svg

rnaseq_ebi

https://github.com/cokelaer/bioservices/actions/workflows/rnaseq_ebi.yml/badge.svg

seqret

https://github.com/cokelaer/bioservices/actions/workflows/seqret.yml/badge.svg

unichem

https://github.com/cokelaer/bioservices/actions/workflows/unichem.yml/badge.svg

uniprot

https://github.com/cokelaer/bioservices/actions/workflows/uniprot.yml/badge.svg

wikipathway

https://github.com/cokelaer/bioservices/actions/workflows/wikipathway.yml/badge.svg

Version

Description

1.8.0

  • add main standalone application.

  • moved chemspider and clinvitae to the attic

  • removed picr service, not active anymore

Release History

This is a summary of the changelog. Complete change can be found in the <main documentation.

1.4.X

  • Include RNASEQ (EBI) in module rnaseq_ebi

  • Renamed kegg.KEGG.info into dbinfo , which was overloaded with Logging

  • Replaced deprecated HGNC with the official web service from genenames.org

  • Fully updated EUtils since WSDL is now down; implementation uses REST now.

  • Removed the apps/taxonomy module now part of http://github.com/biokit.

  • added http_delete in services.py

1.3.X

  • CACHE files are now stored in a general directory in the home, rather than locally

  • Source code moved to github.com

  • New REST class to use requests package instead of urllib2.

  • Creation of a global configuration file in .config/bioservice/bioservices.cfg

  • NEW services: Reactome, Readseq, Ensembl, EUtils

1.2.X

  • add try/except for pandas library.

  • added sub-package called apps with some useful tools (fasta,peptides, taxon) in bioservices.apps directory

  • NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf

1.1.X

  • NEW services: biocarta, pfam, ChEBI, UniChem

  • Add documentation and examples related to Galaxy/BioPython.

  • NEW Service : HGNC

  • Use BeautifulSoup4 instead of 3

1.0.X

  • add PDB, ArrayExpress, biomart, chemspider draft, eutils, miriam, arrayexpress

1.0.0:

  • First release of bioservices

0.9.X:

  • Stable version of bioservices including the following services:

    BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt, WSDbfetch, NCBIblast, PSICQUIC, Wikipath

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