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################################################################################# BIOSERVICES: access to biological web services programmatically #################################################################################

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|Codacy-Grade|

:Python_versionavailable: BioServices is tested for Python 3.9, 3.10, 3.11, 3.12 :Contributions: Please join https://github.com/cokelaer/bioservices :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 <http://bioinformatics.oxfordjournals.org/content/29/24/3241> (2013) 29 (24): 3241-3242 :Documentation: RTD documentation <http://bioservices.readthedocs.io/>_.

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.

Contributors

Maintaining BioServices would not have been possible without users and contributors. Each contribution has been an encouragement to pursue this project. Thanks to all:

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Quick example

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_id:9606", frmt="tsv", limit=3, 
...                 columns="id,length,accession, gene_names")
>>> 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

.. note:: major changes of UniProt API changed all columns names in June 2022. The code above is valid for bioservices versions >1.10. Earlier version used::

    >>> data = u.search("zap70+and+taxonomy:9606", frmt="tab", limit=3, 
    ...                 columns="entry name,length,id, genes")

Note that columns names have changed, the frmt was changed from tab to tsv and taxonomy is now taxonomy_id. Names correspondences can be found in::

    u._legacy_names

More examples and tutorials are available in the On-line documentation <http://bioservices.readthedocs.io/>_

Current services

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

.. note:: Contributions to implement new wrappers are more than welcome. See BioServices github page <https://github.com/cokelaer/bioservices/>_ to join the development, and the Developer guide on how to implement new wrappers.

Bioservices command

In version 1.8.2, we included a bioservices command. For now it has only one subcommand to download a NCBI accession number and possibly it genbank or GFF file (if available)::

bioservices download-accession --accession K01711.1 --with-gbk

Changelog

========= ==================================================================== Version Description ========= ==================================================================== 1.13.0 * Fix pyproject missing requirements

Fix pkg_resources warning
drop python 3.8, add py3.12 1.12.0 migrating to pyproject 1.11.2 Update COG service to be more user-friendly and return all pages by default
uniprot set progress to False in the search method
Merged #250 and #249 user PRs (compress option in uniprot module and logging issue in biodbnet) 1.11.1 Fix regression i uniprot.mapping (https://github.com/cokelaer/bioservices/issues/245) 1.11.0 Fix uniprot limitation of 25 results only (
For developers: all services are now refactorised to use services as an attribute rather than a parent class.
Remove ReactomeOld and ReactomeAnalysis (deprecated)
move rnaseq_ebi (deprecated) to attic for book_keeping 1.10.4 Fix v1.10.3 adding missing requirements.txt 1.10.3 Update pdb service to use v2 API
remove biocarta (website not accesible anymore)
Update Chembl (no API changes) 1.10.2 * Fix #226 and applied PR from Fix from @GianArauz https://github.com/cokelaer/bioservices/pull/232 about UniProt error
Update MANIFEST to fix #232 1.10.1 * allow command line to download genbank and GFF
update pride module to use new PRIDE API (July 2022)
Fixed KEGG bug #225 1.10.0 Update uniprot to use the new API (june 2022) 1.9.0 Update unichem to reflect new API 1.8.4 * biomodels. Fix #208
KEGG: fixed #204 #202 and #203 1.8.3 * Eutils: remove warning due to unreachable URL. Set REST as attribute rather and inheritance.
NEW biocontainers module
KEGG: add save_pathway method. Fix parsing of structure/pdb entry
remove deprecated function from Reactome 1.8.2 Fix suds package in code and requirements 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 1.4.X * NEW RNAseq from EBI in rnaseq_ebi module
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. 1.3.X * CACHE files are now stored in a general directory in the home
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 NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf 1.1.X NEW services: biocarta, pfam, ChEBI, UniChem 1.0.0: first stable release 0.9.X: NEW services: BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt,WSDbfetch, NCBIblast, PSICQUIC, Wikipath ========= ====================================================================

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cokelaer / bioservices

readme

Contributors

Quick example

Current services

Bioservices command

Changelog