bioservices 1.11.2

Description:

bioservices 1.11.2

BIOSERVICES: access to biological web services programmatically







Python_version_available:
BioServices is tested for Python 3.7, 3.8, 3.9, 3.10

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 (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.

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:



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


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


Service
CI testing



arrayexpress



bigg



biocontainers



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



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.



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



1.11.2

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