BioServices

Python version available

BioServices is tested for Python 2.7, 3.3, 3.4, 3.5

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 25 Web Services including. For a quick start, look at some notebooks here github cokelaer/bioservices and here github bioservices.

An up-to-date list of Web Services is provided within the online documentation.

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 exhaustive On-line documentation

Release History

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

1.5.X

• Support for Python 3.6 on Travis.
• No more support for Python 2.6
• biodbnet and wikipathways services now uses the REST protocol (instead of WSDL).
• move readseq to seqret and uses new EBI API
• move wsdbfetch to dbfetch (and switch to REST protocol)
• quickgo uses the new API from EBI
• New Reactome API
• For developers: use pytest instead of nosetests.

1.4.X

• Update uniprot valid column names.
• 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

• 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, PRIDE, clinvitae, Intact (complex)
• CHANGES: all parameters called format have been renamed frmt (to avoid using Python keyword)

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 including the following services: BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt, WSDbfetch, NCBIblast, PSICQUIC, Wikipath