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https://github.com/cokelaer/bioservices

Access to Biological Web Services from Python.
https://github.com/cokelaer/bioservices
biomodels chebi chembl eutils kegg muscle python quickgo unichem uniprot wikipathways
Last synced: 2 months ago
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Access to Biological Web Services from Python.
Host: GitHub
URL: https://github.com/cokelaer/bioservices
Owner: cokelaer
License: other
Created: 2014-08-28T15:24:45.000Z (almost 10 years ago)
Default Branch: main
Last Pushed: 2024-05-03T22:01:23.000Z (2 months ago)
Last Synced: 2024-05-03T23:21:47.848Z (2 months ago)
Topics: biomodels, chebi, chembl, eutils, kegg, muscle, python, quickgo, unichem, uniprot, wikipathways
Language: Python
Homepage: http://bioservices.readthedocs.io
Size: 5.4 MB
Stars: 271
Watchers: 18
Forks: 61
Open Issues: 13
Metadata Files:
- Readme: README.rst
- License: LICENSE
Lists

Awesome-Bioinformatics - bioservices - Access to Biological Web Services from Python. [ [paper-2013](https://academic.oup.com/bioinformatics/article/29/24/3241/194040) | [web](http://bioservices.readthedocs.io) ] (Next Generation Sequencing / Python Modules)
Awesome-Bioinformatics-CN - bioservices - Python访问生物Web服务，如KEGG, BLAST [ [paper-2013](https://academic.oup.com/bioinformatics/article/29/24/3241/194040) | [web](http://bioservices.readthedocs.io) ] (二代测序 / Python包)
README

        .. 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

#################################################################################

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://anaconda.org/conda-forge/bioservices/badges/version.svg   

    :target: https://anaconda.org/conda-forge/bioservices

|Codacy-Grade|

: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:

.. 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 `_

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 `_

    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

========= ====================================================================

.. |Codacy-Grade| image:: https://app.codacy.com/project/badge/Grade/9b8355ff642f4de9acd4b270f8d14d10

   :target: https://app.codacy.com/gh/cokelaer/bioservices/dashboard