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

Pharmacogenomics studies the involvement of interindividual variations in DNA sequence into different drug responses (especially adverse drug reactions). Knowledge Discovery in Databases (KDD) process is a means for discovering new pharmacogenomic knowledge units 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 units 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 SOPharm concepts some well-known examples of pharmacogenomic knowledge.