Skip to main content
This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (pypi.python.org).
Help us improve Python packaging - Donate today!

Access to Biological Web Services from Python

Project Description
BioServices
##############

.. image:: https://badge.fury.io/py/bioservices.svg
:target: https://pypi.python.org/pypi/bioservices

.. image:: https://secure.travis-ci.org/cokelaer/bioservices.png
:target: http://travis-ci.org/cokelaer/bioservices

.. image:: https://coveralls.io/repos/cokelaer/bioservices/badge.png?branch=master
:target: https://coveralls.io/r/cokelaer/bioservices?branch=master

.. image:: https://landscape.io/github/cokelaer/bioservices/master/landscape.png
:target: https://landscape.io/github/cokelaer/bioservices/master

.. image:: http://readthedocs.org/projects/bioservices/badge/?version=master
:target: http://bioservices.readthedocs.org/en/master/?badge=master
:alt: Documentation Status


:Python version available: BioServices is tested for Python 2.6,2.7, 3.3, 3.4, 3.5
:Contributions: Please join https://github.com/cokelaer/bioservices and share your notebooks https://github.com/bioservices/notebooks/
: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).

.. image:: https://raw.githubusercontent.com/cokelaer/bioservices/master/doc/bioservices.png
:target: https://raw.githubusercontent.com/cokelaer/bioservices/master/doc/bioservices.png


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 25 Web Services including. For a quick start,
look at some notebooks here `github cokelaer/bioservices <https://github.com/cokelaer/bioservices/tree/master/notebooks/>`_ and here `github bioservices <https://github.com/bioservices/notebooks`_.

An up-to-date list of Web Services is provided within
the online `documentation <http://pythonhosted.org/bioservices/>`_.

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:9606", frmt="tab", limit=3,
... columns="entry name,length,id, genes")
>>> 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

More examples and tutorials are available in the exhaustive
`On-line documentation <http://pythonhosted.org//bioservices>`_




Release History
------------------
This is a summary of the changelog. Complete change can be found in the
`main documentation <http://pythonhosted.org//bioservices/ChangeLog.html>`_.



1.4.X
---------------

* Update uniprot valid column names.
* Renamed kegg.KEGG.info into dbinfo , which was overloaded with Logging
* 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.
* added http_delete in services.py





1.3.X
+++++++++++

* Source code moved to github.com
* 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, PRIDE, clinvitae, Intact
(complex)
* CHANGES: all parameters called format have been renamed frmt (to avoid using Python keyword)

1.2.X
+++++++++++

* add try/except for pandas library.
* added sub-package called apps with some useful tools (fasta,peptides, taxon) in bioservices.apps directory
* NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf

1.1.X
+++++++++++
* NEW services: biocarta, pfam, ChEBI, UniChem
* Add documentation and examples related to Galaxy/BioPython.
* NEW Service : HGNC
* Use BeautifulSoup4 instead of 3

1.0.X
+++++++++++
* add PDB, ArrayExpress, biomart, chemspider draft, eutils, miriam, arrayexpress

1.0.0
++++++

* First release of bioservices including the following services:
BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt,
WSDbfetch, NCBIblast, PSICQUIC, Wikipath



Release History
------------------
This is a summary of the changelog. Complete change can be found in the
`<main documentation <http://pythonhosted.org//bioservices/ChangeLog.html>`_.




1.4.X
---------------

* Include RNASEQ (EBI) in module rnaseq_ebi
* Renamed kegg.KEGG.info into dbinfo , which was overloaded with Logging
* 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.
* added http_delete in services.py



1.3.X
+++++++++++

* CACHE files are now stored in a general directory in the home, rather than
locally
* Source code moved to github.com
* 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
+++++++++++

* add try/except for pandas library.
* added sub-package called apps with some useful tools (fasta,peptides, taxon) in bioservices.apps directory
* NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf

1.1.X
+++++++++++
* NEW services: biocarta, pfam, ChEBI, UniChem
* Add documentation and examples related to Galaxy/BioPython.
* NEW Service : HGNC
* Use BeautifulSoup4 instead of 3

1.0.X
+++++++++++
* add PDB, ArrayExpress, biomart, chemspider draft, eutils, miriam, arrayexpress

1.0.0:
+++++++++++
* First release of bioservices


0.9.X:
+++++++++++
* Stable version of bioservices including the following services:
BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt,
WSDbfetch, NCBIblast, PSICQUIC, Wikipath

Release History

Release History

This version
History Node

1.5.0

History Node

1.4.17

History Node

1.4.16

History Node

1.4.15

History Node

1.4.14

History Node

1.4.13

History Node

1.4.12

History Node

1.4.11

History Node

1.4.10

History Node

1.4.9

History Node

1.4.8

History Node

1.4.7

History Node

1.4.6

History Node

1.4.5

History Node

1.4.4

History Node

1.4.3

History Node

1.4.2

History Node

1.4.1

History Node

1.4.0

History Node

1.3.7

History Node

1.3.6

History Node

1.3.5

History Node

1.3.4

History Node

1.3.3

History Node

1.3.2

History Node

1.3.1

History Node

1.3.0

History Node

1.2.6

History Node

1.2.5

History Node

1.2.4

History Node

1.2.3

History Node

1.2.2

History Node

1.2.1

History Node

1.2.0

History Node

1.1.3

History Node

1.1.2

History Node

1.1.1

History Node

1.1.0

History Node

1.0.4

History Node

1.0.3

History Node

1.0.2

History Node

1.0.1

History Node

1.0.0

Download Files

Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
bioservices-1.5.0.tar.gz (218.9 kB) Copy SHA256 Checksum SHA256 Source Oct 25, 2017

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting