#################################################################################
BIOSERVICES: access to biological web services programmatically
#################################################################################
.. image:: https://badge.fury.io/py/bioservices.svg
:target: https://pypi.python.org/pypi/bioservices
.. image:: https://github.com/cokelaer/bioservices/actions/workflows/ci.yml/badge.svg
:target: https://github.com/cokelaer/bioservices/actions/workflows/ci.yml
.. image:: http://readthedocs.org/projects/bioservices/badge/?version=main
:target: http://bioservices.readthedocs.org/en/main/?badge=main
:alt: Documentation Status
.. image:: https://static.pepy.tech/personalized-badge/bioservices?period=month&units=international_system&left_color=black&right_color=orange&left_text=Downloads
:target: https://pepy.tech/project/bioservices
.. image:: https://raw.githubusercontent.com/cokelaer/bioservices/main/doc/_static/bioservices2_logo_256.png
:target: https://raw.githubusercontent.com/cokelaer/bioservices/main/doc/_static/bioservices2_logo_256.png
: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 <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_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.
==================== ================================================================================================
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
biocontainers .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biocontainers.yml/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
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
========= ====================================================================
1.11.1 * 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
========= ====================================================================
Raw data
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"description": "#################################################################################\nBIOSERVICES: access to biological web services programmatically\n#################################################################################\n\n\n.. image:: https://badge.fury.io/py/bioservices.svg\n :target: https://pypi.python.org/pypi/bioservices\n\n.. image:: https://github.com/cokelaer/bioservices/actions/workflows/ci.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/ci.yml\n\n.. image:: http://readthedocs.org/projects/bioservices/badge/?version=main\n :target: http://bioservices.readthedocs.org/en/main/?badge=main\n :alt: Documentation Status\n\n.. image:: https://static.pepy.tech/personalized-badge/bioservices?period=month&units=international_system&left_color=black&right_color=orange&left_text=Downloads\n :target: https://pepy.tech/project/bioservices\n\n.. image:: https://raw.githubusercontent.com/cokelaer/bioservices/main/doc/_static/bioservices2_logo_256.png\n :target: https://raw.githubusercontent.com/cokelaer/bioservices/main/doc/_static/bioservices2_logo_256.png\n\n\n:Python_version_available: BioServices is tested for Python 3.7, 3.8, 3.9, 3.10\n:Contributions: Please join https://github.com/cokelaer/bioservices \n:Issues: Please use https://github.com/cokelaer/bioservices/issues\n:How to cite: Cokelaer et al. *BioServices: a common Python package to access biological Web Services programmatically*\n `Bioinformatics <http://bioinformatics.oxfordjournals.org/content/29/24/3241>`_ (2013) 29 (24): 3241-3242\n:Documentation: `RTD documentation <http://bioservices.readthedocs.io/>`_.\n\n**Bioservices** is a Python package that provides access to many Bioinformatices Web Services (e.g.,\nUniProt) and a framework to easily implement Web Services wrappers (based on \nWSDL/SOAP or REST protocols).\n\n\nThe primary goal of **BioServices** is to use Python as a glue language to provide\na programmatic access to several Bioinformatics Web Services. By doing so, elaboration of new\napplications that combine several of the wrapped Web Services is fostered.\n\nOne of the main philosophy of **BioServices** is to make use of the existing\nbiological databases (not to re-invent new databases) and to alleviates the\nneeds for expertise in Web Services for the developers/users.\n\nBioServices provides access to about 40 Web Services. \n\nContributors\n============\n\nMaintaining BioServices would not have been possible without users and contributors. \nEach contribution has been an encouragement to pursue this project. Thanks to all:\n\n.. image:: https://contrib.rocks/image?repo=cokelaer/bioservices\n :target: https://github.com/cokelaer/bioservices/graphs/contributors\n\n\nQuick example\n=============\n\nHere is a small example using the UniProt Web Service to search for the zap70 specy in human\norganism::\n\n >>> from bioservices import UniProt\n >>> u = UniProt(verbose=False)\n >>> data = u.search(\"zap70+and+taxonomy_id:9606\", frmt=\"tsv\", limit=3, \n ... columns=\"id,length,accession, gene_names\")\n >>> print(data)\n Entry name Length Entry Gene names\n ZAP70_HUMAN 619 P43403 ZAP70 SRK\n B4E0E2_HUMAN 185 B4E0E2\n RHOH_HUMAN 191 Q15669 RHOH ARHH TTF\n\n\n.. note:: major changes of UniProt API changed all columns names in June 2022. The code above is valid for bioservices\n versions >1.10. Earlier version used::\n\n >>> data = u.search(\"zap70+and+taxonomy:9606\", frmt=\"tab\", limit=3, \n ... columns=\"entry name,length,id, genes\")\n\n Note that columns names have changed, the frmt was changed from tab to tsv \n and taxonomy is now taxonomy_id. Names correspondences can be found in::\n\n u._legacy_names\n\n\nMore examples and tutorials are available in the `On-line documentation <http://bioservices.readthedocs.io/>`_\n\nCurrent services\n================\nHere is the list of services available and their testing status.\n\n\n==================== ================================================================================================\nService CI testing\n==================== ================================================================================================\narrayexpress .. image:: https://github.com/cokelaer/bioservices/actions/workflows/arrayexpress.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/arrayexpress.yml\nbigg .. image:: https://github.com/cokelaer/bioservices/actions/workflows/bigg.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/bigg.yml\nbiocontainers .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biocontainers.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/biocontainers.yml\nbiodbnet .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biodbnet.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/biodbnet.yml\nbiogrid .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biogrid.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/biogrid.yml\nbiomart .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biomart.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/biomart.yml\nbiomodels .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biomodels.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/biomodels.yml\nchebi .. image:: https://github.com/cokelaer/bioservices/actions/workflows/chebi.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/chebi.yml\nchembl .. image:: https://github.com/cokelaer/bioservices/actions/workflows/chembl.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/chembl.yml\ncog .. image:: https://github.com/cokelaer/bioservices/actions/workflows/cog.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/cog.yml\ndbfetch .. image:: https://github.com/cokelaer/bioservices/actions/workflows/dbfetch.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/dbfetch.yml\nena .. image:: https://github.com/cokelaer/bioservices/actions/workflows/ena.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/ena.yml\nensembl .. image:: https://github.com/cokelaer/bioservices/actions/workflows/ensembl.yml/badge.svg\n :target: 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https://github.com/cokelaer/bioservices/actions/workflows/seqret.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/seqret.yml\nunichem .. image:: https://github.com/cokelaer/bioservices/actions/workflows/unichem.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/unichem.yml\nuniprot .. image:: https://github.com/cokelaer/bioservices/actions/workflows/uniprot.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/uniprot.yml\nwikipathway .. image:: https://github.com/cokelaer/bioservices/actions/workflows/wikipathway.yml/badge.svg\n :target: https://github.com/cokelaer/bioservices/actions/workflows/wikipathway.yml\n==================== ================================================================================================\n\n.. note:: Contributions to implement new wrappers are more than welcome. \n See `BioServices github page <https://github.com/cokelaer/bioservices/>`_\n to join the development, and the Developer guide on how to implement new\n wrappers.\n\nBioservices command\n====================\n\nIn 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)::\n\n bioservices download-accession --accession K01711.1 --with-gbk \n\n\nChangelog\n=========\n\n\n========= ====================================================================\nVersion Description\n========= ====================================================================\n1.11.1 * Fix regression i uniprot.mapping \n (https://github.com/cokelaer/bioservices/issues/245)\n1.11.0 * Fix uniprot limitation of 25 results only (\n * For developers: all services are now refactorised to use services\n as an attribute rather than a parent class.\n * Remove ReactomeOld and ReactomeAnalysis (deprecated)\n * move rnaseq_ebi (deprecated) to attic for book_keeping\n1.10.4 * Fix v1.10.3 adding missing requirements.txt\n1.10.3 * Update pdb service to use v2 API\n * remove biocarta (website not accesible anymore)\n * Update Chembl (no API changes)\n1.10.2 * Fix #226 and applied PR from Fix from @GianArauz\n https://github.com/cokelaer/bioservices/pull/232 about UniProt \n error\n * Update MANIFEST to fix #232\n1.10.1 * allow command line to download genbank and GFF\n * update pride module to use new PRIDE API (July 2022)\n * Fixed KEGG bug #225\n1.10.0 * Update uniprot to use the new API (june 2022)\n1.9.0 * Update unichem to reflect new API\n1.8.4 * biomodels. Fix #208\n * KEGG: fixed #204 #202 and #203\n1.8.3 * Eutils: remove warning due to unreachable URL. Set REST as\n attribute rather and inheritance. \n * NEW biocontainers module\n * KEGG: add save_pathway method. Fix parsing of structure/pdb entry\n * remove deprecated function from Reactome\n1.8.2 * Fix suds package in code and requirements\n1.8.1 * Integrated a change made in KEGG service (DEFINITON was changed to\n ORG_CODE)\n * for developers: applied black on all modules\n * switch suds-jurko to new suds community \n1.8.0 * add main standalone application. \n * moved chemspider and clinvitae to the attic\n * removed picr service, not active anymore\n1.4.X * NEW RNAseq from EBI in rnaseq_ebi module\n * Replaced deprecated HGNC with the official web service from genenames.org\n * Fully updated EUtils since WSDL is now down; implementation uses REST now.\n * Removed the apps/taxonomy module now part of http://github.com/biokit. \n1.3.X * CACHE files are now stored in a general directory in the home\n * New REST class to use **requests** package instead of urllib2. \n * Creation of a global configuration file in .config/bioservice/bioservices.cfg\n * NEW services: Reactome, Readseq, Ensembl, EUtils\n1.2.X * NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf\n1.1.X * NEW services: biocarta, pfam, ChEBI, UniChem\n1.0.0: * first stable release\n0.9.X: * NEW services: BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, \n Rhea, UniProt,WSDbfetch, NCBIblast, PSICQUIC, Wikipath\n========= ====================================================================",
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