Suggested Ontology for Pharmacogenomics (SO-Pharm): Modular Construction and Preliminary Testing

Adrien Coulet (1, 2) , Malika Smaïl-Tabbone (1) , Amedeo Napoli (1) , Marie-Dominique Devignes (1)

1 ORPAILLEUR - Knowledge representation, reasonning
2 KIKA MEDICAL - KIKA medical

Pharmacogenomics studies the involvement of interindivid- ual 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.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Base de données [cs.DB]

Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes. Suggested Ontology for Pharmacogenomics (SO-Pharm): Modular Construction and Preliminary Testing. Proceedings of International Workshop on Knowledge Systems in Bioinformatics - KSinBIT'06, Oct 2006, Montpellier, France. ⟨inria-00089824⟩