bioservices

Access to Biological Web Services from Python.

https://github.com/cokelaer/bioservices

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
✓
Committers with academic emails
5 of 30 committers (16.7%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.4%) to scientific vocabulary

Keywords

biomodels chebi chembl eutils kegg muscle python quickgo unichem uniprot wikipathways

Keywords from Contributors

bioinformatics genomes rdf interactive sequences blackhole standards usegalaxy serializer ngs

Last synced: 6 months ago · JSON representation

Repository

Access to Biological Web Services from Python.

Basic Info

Host: GitHub
Owner: cokelaer
License: other
Language: Python
Default Branch: main
Homepage: http://bioservices.readthedocs.io
Size: 6.33 MB

Statistics

Stars: 310
Watchers: 17
Forks: 64
Open Issues: 17
Releases: 23

Topics

biomodels chebi chembl eutils kegg muscle python quickgo unichem uniprot wikipathways

Created over 11 years ago · Last pushed 7 months ago

Metadata Files

Readme License

README.rst

.. 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 3.9, 3.10, 3.11, 3.12
: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
========= ====================================================================
1.12.1    * fix pyproject to use python>3.9 and pandas/numpy>2.2
1.12.0    * Fix pyproject missing requirements
          * Fix pkg_resources warning
          * drop python 3.8, add py3.12
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

Owner

Name: Thomas Cokelaer
Login: cokelaer
Kind: user
Location: Paris, France
Company: Institut Pasteur

Website: http://thomas-cokelaer.info/
Twitter: ThomasCokelaer
Repositories: 62
Profile: https://github.com/cokelaer

Bioinformatician, Scientific Software Developer, Python developer

GitHub Events

Total

Create event: 5
Release event: 2
Issues event: 5
Watch event: 32
Delete event: 5
Issue comment event: 1
Push event: 16
Pull request event: 9
Fork event: 3

Last Year

Create event: 5
Release event: 2
Issues event: 5
Watch event: 32
Delete event: 5
Issue comment event: 1
Push event: 16
Pull request event: 9
Fork event: 3

Committers

Last synced: 9 months ago

All Time

Total Commits: 1,167
Total Committers: 30
Avg Commits per committer: 38.9
Development Distribution Score (DDS): 0.107

Past Year

Commits: 17
Committers: 2
Avg Commits per committer: 8.5
Development Distribution Score (DDS): 0.294

Top Committers

Name	Email	Commits
Thomas Cokelaer	c**r@g**m	1,042
Jordi SMusach	j**h@g**m	25
Dennis Pultz	dp@b****k	20
thoba	l**a@g**m	18
Lea Harder	l**h@b**k	15
dependabot[bot]	4****]	10
Achilles Rasquinha	a**a@g**m	4
Erik White	2****e	3
Patrick Short	p**2@g**m	3
Saahith Pochiraju	s**6@g**m	3
Yury Kirienko	y**o@g**m	2
Fabian Rost	f**t@p**e	2
Gian Arauz	g**z@g**m	2
Nick Weiner	b**r@u**u	2
bryan brancotte	b**e@p**r	1
Sujay Patil	s**l@g**m	1
Maurice Althoff	s**f@t**m	1
Yury Kirienko	i**o@e**m	1
nmih	n**h@u**u	1
vincent	v**l@b**r	1
Sebastian Lobentanzer	s**r@g**m	1
PoorRican	5****n	1
Lucian Smith	l**h@u**u	1
Leonardo Gama	l**a@g**m	1
Josh Loecker	j**r@i**m	1
Joseph Bonello	b****9	1
Hervé Ménager	h**r@g**m	1
G Fedewa	g**a@n**m	1
David Schryer	s**r@g**m	1
Arnaud Belcour	a**r@i**r	1

Committer Domains (Top 20 + Academic)

bmb.sdu.dk: 2 irisa.fr: 1 nuancedhealth.com: 1 uw.edu: 1 butantan.gov.br: 1 ucsd.edu: 1 epam.com: 1 test.com: 1 pasteur.fr: 1 ucdavis.edu: 1 pks.mpg.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 88
Total pull requests: 36
Average time to close issues: 8 months
Average time to close pull requests: 4 months
Total issue authors: 66
Total pull request authors: 13
Average comments per issue: 1.73
Average comments per pull request: 0.58
Merged pull requests: 28
Bot issues: 0
Bot pull requests: 16

Past Year

Issues: 4
Pull requests: 7
Average time to close issues: N/A
Average time to close pull requests: about 1 month
Issue authors: 2
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 7

View more stats

Top Authors

Issue Authors

cokelaer (12)
a-r-j (3)
antonkulaga (2)
nc1m (2)
smdabdoub (2)
GianArauz (2)
willigott (2)
timbitz (2)
JoshLoecker (2)
luciansmith (2)
joaquinabian (2)
johnnytam100 (1)
achillesrasquinha (1)
jjczajka (1)
thudxz (1)

Pull Request Authors

dependabot[bot] (25)
cokelaer (8)
GianArauz (2)
Erik-White (1)
ArnaudBelcour (1)
fbnrst (1)
lowrymj (1)
luciansmith (1)
JoshLoecker (1)
leogama (1)
harper357 (1)
slobentanzer (1)
PoorRican (1)

Top Labels

Issue Labels

question (5) wontfix (4) Service-side issue(not bioservices) (3) enhancement (3) bug (2) help wanted (2) in progress (1)

Pull Request Labels

dependencies (25) python (5)

Packages

Total packages: 3
Total downloads:
- pypi 17,764 last-month
Total docker downloads: 498

Total dependent packages: 20
(may contain duplicates)
Total dependent repositories: 89
(may contain duplicates)
Total versions: 101
Total maintainers: 1

pypi.org: bioservices

Access to Biological Web Services from Python

Homepage: https://bioservices.readthedocs.io
Documentation: https://bioesrvices.readthedocs.io
License: GPLv3
Latest release: 1.12.1
published 12 months ago

Versions: 75
Dependent Packages: 20
Dependent Repositories: 87
Downloads: 17,764 Last month
Docker Downloads: 498

Rankings

Dependent packages count: 0.6%

Dependent repos count: 1.6%

Average: 3.1%

Downloads: 3.2%

Stargazers count: 3.9%

Docker downloads count: 4.0%

Forks count: 5.4%

Maintainers (1)

cokelaer

Last synced: 6 months ago

proxy.golang.org: github.com/cokelaer/bioservices

Documentation: https://pkg.go.dev/github.com/cokelaer/bioservices#section-documentation
License: other
Latest release: v1.12.1
published about 1 year ago

Versions: 19
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 9.0%

Average: 9.6%

Dependent repos count: 10.2%

Last synced: 6 months ago

conda-forge.org: bioservices

Homepage: https://github.com/cokelaer/bioservices
License: GPL-3.0-only
Latest release: 1.10.0
published over 3 years ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 2

Rankings

Dependent repos count: 20.2%

Forks count: 23.1%

Stargazers count: 24.0%

Average: 29.7%

Dependent packages count: 51.6%

Last synced: 6 months ago

Dependencies

.github/workflows/arrayexpress.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/arrayexpressbigg.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/bigg.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/biocontainers.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/biodbnet.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/biogrid.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/biomart.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/biomodels.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/chebi.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/chembl.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/ci.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/cog.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/dbfetch.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/ena.yml actions

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requirements.txt pypi

appdirs *
beautifulsoup4 *
colorlog *
easydev >=0.12.0
grequests *
lxml *
matplotlib *
pandas >=0.21.1
requests *
requests_cache *
suds-community >=0.7
tqdm *
wrapt *
xmltodict *

requirements_dev.txt pypi

coveralls * development
easydev * development
flaky * development
ipython * development
numpydoc * development
pytest * development
pytest-cov * development
pytest-runner * development
pytest-timeout * development
pytest-xdist * development
sphinx * development
sphinx-copybutton * development
sphinx-gallery * development
sphinx_rtd_theme * development

setup.py pypi

grequests *