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

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: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 <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:

.. image:: https://contrib.rocks/image?repo=cokelaer/bioservices :target: https://github.com/cokelaer/bioservices/graphs/contributors

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: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 <http://bioservices.readthedocs.io/>_

Current services

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

==================== ================================================================================================ Service CI testing ==================== ================================================================================================ arrayexpress .. image:: https://github.com/cokelaer/bioservices/actions/workflows/arrayexpress.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/arrayexpress.yml bigg .. image:: https://github.com/cokelaer/bioservices/actions/workflows/bigg.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/bigg.yml biocarta .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biocarta.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/biocarta.yml biocontainers .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biocontainersyml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/biocontainers.yml biodbnet .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biodbnet.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/biodbnet.yml biogrid .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biogrid.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/biogrid.yml biomart .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biomart.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/biomart.yml biomodels .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biomodels.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/biomodels.yml chebi .. image:: https://github.com/cokelaer/bioservices/actions/workflows/chebi.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/chebi.yml chembl .. image:: https://github.com/cokelaer/bioservices/actions/workflows/chembl.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/chembl.yml cog .. image:: https://github.com/cokelaer/bioservices/actions/workflows/cog.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/cog.yml dbfetch .. image:: https://github.com/cokelaer/bioservices/actions/workflows/dbfetch.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/dbfetch.yml ena .. image:: https://github.com/cokelaer/bioservices/actions/workflows/ena.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/ena.yml ensembl .. image:: https://github.com/cokelaer/bioservices/actions/workflows/ensembl.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/ensembl.yml eutils .. image:: https://github.com/cokelaer/bioservices/actions/workflows/eutils.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/eutils.yml eva .. image:: https://github.com/cokelaer/bioservices/actions/workflows/eva.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/eva.yml hgnc .. image:: https://github.com/cokelaer/bioservices/actions/workflows/hgnc.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/hgnc.yml intact_complex .. image:: https://github.com/cokelaer/bioservices/actions/workflows/intact_complex.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/intact_complex.yml kegg .. image:: https://github.com/cokelaer/bioservices/actions/workflows/kegg.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/kegg.yml muscle .. image:: https://github.com/cokelaer/bioservices/actions/workflows/muscle.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/muscle.yml mygeneinfo .. image:: https://github.com/cokelaer/bioservices/actions/workflows/mygeneinfo.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/mygeneinfo.yml ncbiblast .. image:: https://github.com/cokelaer/bioservices/actions/workflows/ncbiblast.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/ncbiblast.yml omicsdi .. image:: https://github.com/cokelaer/bioservices/actions/workflows/omicsdi.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/omicsdi.yml omnipath .. image:: https://github.com/cokelaer/bioservices/actions/workflows/omnipath.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/omnipath.yml panther .. image:: https://github.com/cokelaer/bioservices/actions/workflows/panther.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/panther.yml pathwaycommons .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pathwaycommons.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/pathwaycommons.yml pdb .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pdb.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/pdb.yml pdbe .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pdbe.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/pdbe.yml pfam .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pfam.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/pfam.yml pride .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pride.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/pride.yml psicquic .. image:: https://github.com/cokelaer/bioservices/actions/workflows/psicquic.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/psicquic.yml pubchem .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pubchem.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/pubchem.yml quickgo .. image:: https://github.com/cokelaer/bioservices/actions/workflows/quickgo.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/quickgo.yml reactome .. image:: https://github.com/cokelaer/bioservices/actions/workflows/reactome.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/reactome.yml rhea .. image:: https://github.com/cokelaer/bioservices/actions/workflows/rhea.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/rhea.yml rnaseq_ebi .. image:: https://github.com/cokelaer/bioservices/actions/workflows/rnaseq_ebi.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/rnaseq_ebi.yml seqret .. image:: https://github.com/cokelaer/bioservices/actions/workflows/seqret.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/seqret.yml unichem .. image:: https://github.com/cokelaer/bioservices/actions/workflows/unichem.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/unichem.yml uniprot .. image:: https://github.com/cokelaer/bioservices/actions/workflows/uniprot.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/uniprot.yml wikipathway .. image:: https://github.com/cokelaer/bioservices/actions/workflows/wikipathway.yml/badge.svg :target: https://github.com/cokelaer/bioservices/actions/workflows/wikipathway.yml ==================== ================================================================================================

.. 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 ========= ==================================================================== 1.10.1 * allow command line to download genbank and GFF * update pride module to use new PRIDE API (July 2022) 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 ========= ====================================================================