bioservices 1.8.1

Access to Biological Web Services from Python

Python_version_available:

BioServices is tested for Python 3.6, 3.7, 3.8, 3.9

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
bigg
biocarta
biodbnet
biogrid
biomart
biomodels
chebi
chembl
cog
dbfetch
ena
ensembl
eutils
eva
hgnc
intact_complex
kegg
muscle
mygeneinfo
ncbiblast
omicsdi
omnipath
panther
pathwaycommons
pdb
pdbe
pfam
pride
psicquic
pubchem
quickgo
reactome
rhea
rnaseq_ebi
seqret
unichem
uniprot
wikipathway

Note

Contributions to implement new wrappers are more than welcome. See BioServices github page to join the development, and the Developer guide on how to implement new wrappers.

Version	Description
1.8.1	Integrated a change made in KEGG service (DEFINITON was changed to ORG_CODE) for developers: applied black on all modules switch suds-jurko to new suds community
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