bioservices 1.7.5

Access to Biological Web Services from Python

Python_version_available:

BioServices is tested for Python 2.7, 3.6, 3.7

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.

Revision 1.7.0

• General fixes and update from @thobalose (https://github.com/cokelaer/bioservices/pull/149) to updating matplotlib to 3.0.3

• added panther module (pantherdb.org)

• added tests for pubchem, pfam and eva modules, which are still in draft version though

• deprecated PICR and TCGA modules (the latter was not really available anyway)

• Fixed wikipathway, kegg, reactome tests and code (issues 148 and 151)

1.6.X

• rewrote entirely the ChEMBL wrapper due to new ChEMBL API.

• removed the quickgo_old module and its tests

• Fix typo for a “valid colum,” in uniprot module

• Changed biomodels WSDL endpoint (thanks to https://github.com/thobalose. )

• uses colorlog to have more robust and consistent logging.

• Fixed wikipathway XML issues by outputing dictionaries now. This fixes

  https://github.com/cokelaer/bioservices/issues/131

• Fix https://github.com/cokelaer/bioservices/issues/137 to handle KEGG GENE field properly in KEGGParse

• Fix https://github.com/cokelaer/bioservices/issues/125 thanks to

  https://github.com/thobalose.

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

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