Python API for EVS Konrad Rokicki, SAIC. Python Programming Language Dynamic, object-oriented, open-source Cross-platform, popular for scripting Extensive.

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Presentation transcript:

Python API for EVS Konrad Rokicki, SAIC

Python Programming Language Dynamic, object-oriented, open-source Cross-platform, popular for scripting Extensive standard libraries and large open source community Strong support for scientific computing (SciPy, python(x,y), Matplotlib) Gaining popularity in bioinformatics (Biopython, Pygr) See also A Primer on Python for Life Science Researchers Python course in Bioinformatics Biopython python(x,y)

pyCaCORE Code generator and client library 1.Generates a complete Python API from a WSDL file 2.Generated API uses pyCaCORE as a client library (for features like proxying, caching, association navigation, compatibility with Axis) Built on top of ZSI (Zolera SOAP Infrastructure) Originally built to generate caBIO Python API Now tested with EVS This required modifications to support eager loading of associations

ZSI pyEVS Architecture EVS Server Web Service Endpoint SOAP Request SOAP Response wsdl2py- generated API pyEVS User Code AxisReader Axis ServerClient

pyEVS API from cabig.evs.service import * s = EVSApplicationService() m = MetaThesaurusConcept(name='NCBI') results = s.queryObject(MetaThesaurusConcept.className, m) for r in results: print r.cui, r.name print "Synonyms:",‘; '.join(r.synonymCollection)

Output C NCBI_taxonomy Synonyms: NCBI_taxonomy; National Center for Biotechnology Information; NCBI Taxonomy; NCBI; root (of NCBI Taxonomy); NCBI Taxonomy; NCBI Taxonomy; NCBI; root (of NCBI Taxonomy) C NCBI Taxonomy, 2006_01_04 Synonyms: NCBI Taxonomy, 2006_01_04; NCBI2006_01_04 CL NCBI_Taxon_ID Synonyms: NCBI_Taxon_ID

No association traversal d = DescLogicConcept(name='intronic') results = s.queryObject(d.className, d) Next line generates error: “This service does not support the getAssociation method.” results[0].propertyCollection Instead, do this: propertyCollection = s.queryObject(Property.className, d)

No tree traversal d = DescLogicConcept(name='intron') results = s.queryObject(d.className, d) d = results[0] d.name is “Intron” d.code is “C13249” But what is the super concept? NCI Term Browser says “Gene Feature” (C13445) Not possible to retrieve with web services.

Resources Distribution: pyCaBIG Gforge Also available in SVN Documentation: NCICB WIKI Related Feature Requests [#15091] Implement getAssociation for EVS API web service [#15092] Implement tree browsing for web services