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Access to Biological Web Services from Python

Project description

Bioservices provides a framework to easily implement wrapper of Web Services. It focuses on Biological Web Services based 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 Web Services. By doing so, elaboration of new applications that combine several of the wrapped Web Services should be fostered.

One of the main philosophy of BioServices is to make use of the existing SOAP/WSDL facilities provided in biological databases, not to re-invent new databases.

So far, BioServices provides wrappers for about 10 Web Services including KEGG, UniProt, BioModels, WikiPathway, quickGO, PSIQUIC.

Example using the UniProt Web Service to search for the zap70 specy in human organism:

>>> from bioservices import UniProt
>>> u = UniProt(verbose=False)
>>> data ="zap70+and+taxonomy:9606", format="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

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