Package: bioservices
BIOSERVICES: access to biological web services programmaticallyPython_version_available:BioServices is tested for Python 3.7, 3.8, 3.9, 3.10Contributions:Please joinhttps://github.com/cokelaer/bioservicesIssues:Please usehttps://github.com/cokelaer/bioservices/issuesHow to cite:Cokelaer et al.BioServices: a common Python package to access biological Web Services programmaticallyBioinformatics(2013) 29 (24): 3241-3242Documentation:RTD documentation.Bioservicesis 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 ofBioServicesis 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 ofBioServicesis 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.ContributorsMaintaining BioServices would not have been possible without users and contributors.
Each contribution has been an encouragement to pursue this project. Thanks to all:Quick exampleHere 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 TTFNotemajor 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_namesMore examples and tutorials are available in theOn-line documentationCurrent servicesHere is the list of services available and their testing status.ServiceCI testingarrayexpressbiggbiocontainersbiodbnetbiogridbiomartbiomodelschebichemblcogdbfetchenaensembleutilsevahgncintact_complexkeggmusclemygeneinfoncbiblastomicsdiomnipathpantherpathwaycommonspdbpdbepfampridepsicquicpubchemquickgoreactomerheaseqretunichemuniprotwikipathwayNoteContributions to implement new wrappers are more than welcome.
SeeBioServices github pageto join the development, and the Developer guide on how to implement new
wrappers.Bioservices commandIn 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-gbkChangelogVersionDescription1.11.2Update COG service to be more user-friendly and return all pages
by defaultuniprot set progress to False in the search methodMerged #250 and #249 user PRs (compress option in uniprot module
and logging issue in biodbnet)1.11.1Fix regression i uniprot.mapping
(https://github.com/cokelaer/bioservices/issues/245)1.11.0Fix 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_keeping1.10.4Fix v1.10.3 adding missing requirements.txt1.10.3Update pdb service to use v2 APIremove biocarta (website not accesible anymore)Update Chembl (no API changes)1.10.2Fix #226 and applied PR from Fix from @GianArauzhttps://github.com/cokelaer/bioservices/pull/232about UniProt
errorUpdate MANIFEST to fix #2321.10.1allow command line to download genbank and GFFupdate pride module to use new PRIDE API (July 2022)Fixed KEGG bug #2251.10.0Update uniprot to use the new API (june 2022)1.9.0Update unichem to reflect new API1.8.4biomodels. Fix #208KEGG: fixed #204 #202 and #2031.8.3Eutils: remove warning due to unreachable URL. Set REST as
attribute rather and inheritance.NEW biocontainers moduleKEGG: add save_pathway method. Fix parsing of structure/pdb entryremove deprecated function from Reactome1.8.2Fix suds package in code and requirements1.8.1Integrated a change made in KEGG service (DEFINITON was changed to
ORG_CODE)for developers: applied black on all modulesswitch suds-jurko to new suds community1.8.0add main standalone application.moved chemspider and clinvitae to the atticremoved picr service, not active anymore1.4.XNEW RNAseq from EBI in rnaseq_ebi moduleReplaced deprecated HGNC with the official web service from genenames.orgFully updated EUtils since WSDL is now down; implementation uses REST now.Removed the apps/taxonomy module now part ofhttp://github.com/biokit.1.3.XCACHE files are now stored in a general directory in the homeNew REST class to userequestspackage instead of urllib2.Creation of a global configuration file in .config/bioservice/bioservices.cfgNEW services: Reactome, Readseq, Ensembl, EUtils1.2.XNEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf1.1.XNEW services: biocarta, pfam, ChEBI, UniChem1.0.0:first stable release0.9.X:NEW services: BioModels, Kegg, Reactome, Chembl, PICR, QuickGO,
Rhea, UniProt,WSDbfetch, NCBIblast, PSICQUIC, Wikipath