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 Researchershttp://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0030199

• Python course in Bioinformaticshttp://www.pasteur.fr/recherche/unites/sis/formation/python/

• Biopythonhttp://biopython.org/wiki/Main_Page

• python(x,y)http://www.pythonxy.com/foreword.php

pyCaCORE

• Code generator and client library 1. Generates a complete Python API from a WSDL file2. 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

AxisReaderAxis

Server Client

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

C0995203 NCBI_taxonomySynonyms: NCBI_taxonomy; National Center for Biotechnology

Information; NCBI Taxonomy; NCBI; root (of NCBI Taxonomy); NCBI Taxonomy; NCBI Taxonomy; NCBI; root (of NCBI Taxonomy)

C1621796 NCBI Taxonomy, 2006_01_04Synonyms: NCBI Taxonomy, 2006_01_04; NCBI2006_01_04

CL357298 NCBI_Taxon_IDSynonyms: 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• http://gforge.nci.nih.gov/frs/?group_id=525&release_id=2586

• Also available in SVNhttps://gforge.nci.nih.gov/svnroot/pycabig/pyevs/trunk

• Documentation: NCICB WIKI• https://wiki.nci.nih.gov/display/caCORE/EVS+Python+API• https://wiki.nci.nih.gov/display/caCORE/Python+API+Generation

• Related Feature Requests• [#15091] Implement getAssociation for EVS API web service

http://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=15091• [#15092] Implement tree browsing for web services

http://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=15092

http://cabioapi.nci.nih.gov/cabio40/services/caBIOService?wsdl