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bioservices 1.5.0

Access to Biological Web Services from Python

BioServices
##############

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: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
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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`_.<br="">
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

 
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