Suggested ontology for pharmacogenomics (SO-Pharm): modular construction and preliminary testing

Authors:
Adrien Coulet;Malika Smaïl-Tabbone;Amedeo Napoli;Marie-Dominique Devignes
Affiliations:
KIKA Medical, Paris, France;LORIA (UMR 7503 CNRS-INPL-INRIA-Nancy2-UHP), Vandoeuvre-lès-Nancy, France;LORIA (UMR 7503 CNRS-INPL-INRIA-Nancy2-UHP), Vandoeuvre-lès-Nancy, France;LORIA (UMR 7503 CNRS-INPL-INRIA-Nancy2-UHP), Vandoeuvre-lès-Nancy, France
Venue:
OTM'06 Proceedings of the 2006 international conference on On the Move to Meaningful Internet Systems: AWeSOMe, CAMS, COMINF, IS, KSinBIT, MIOS-CIAO, MONET - Volume Part I
Year:
2006

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Abstract

Pharmacogenomics studies the involvement of interindividual variations of DNA sequence in different drug responses (especially adverse drug reactions) Knowledge Discovery in Databases (KDD) process is a means for discovering new pharmacogenomic knowledge in biological databases However data complexity makes it necessary to guide the KDD process by representation of domain knowledge Three domains at least are in concern: genotype, drug and phenotype The approach described here aims at reusing whenever possible existing domain knowledge in order to build a modular formal representation of domain knowledge in pharmacogenomics The resulting ontology is called SO-Pharm for Suggested Ontology for Pharmacogenomics Various situations encountered during the construction process are analyzed and discussed A preliminary validation is provided by representing with SO-Pharm concepts some well-known examples of pharmacogenomic knowledge.