MODELING THE PHARMACOGENOMICS OF DEPRESSION.ppt

HCLS2008 @ WWW2008 HCLS2008 @ WWW2008 HCLS2008 @ WWW2008 MODELING THE PHARMACOGENOMICS OF DEPRESSION Michel Dumontier, Muhammad Faizan, Joseph Obeng, Natalia Villanueva-Rosales Carleton University HCLS2008 @ WWW2008 * “If it were not for the great variability among individuals, medicine might as well be a science and not an art” Sir William Osler, 1892 Pharmacogenomics: The application of genomics to the study of human variability in drug response HCLS2008 @ WWW2008 * PERSONALIZED MEDICINE The ability to offer The Right Drug To The Right Patient For The Right Disease At The Right Time With The Right Dosage HCLS2008 @ WWW2008 * PHARMGKB +Role of genes, gene variants , drugs +pharmacokinetics +pharmacodynamics + clinical outcomes. + Links to publications - Natural language descriptions - Variant details in publications HCLS2008 @ WWW2008 * SOPHARM Suggested Ontology for Pharmacogenomics + OWL ontology +/- Ontology reuse High complexity 14 ontologies: ChEBI, PATO, Unit Ontology, Disease Ontology, Mammalian Phenotype Ontology, MEO, Sequence Ontology, SNP-Ontology, Amino-Acid Ontology, Family Bond Ontology, Pharmacogenetics Ontology, Relationship Ontology and CTO/OBI (Ontology of Clinical Investigation) SOPHARM: 70 classes, 56 properties OTHER: 84786 classes, 189 properties - Very expensive to reason with HCLS2008 @ WWW2008 * Pharmacogenomics Ontology: simpler knowledge representation Pharmacogenomics of Depression: explicit knowledge representation HCLS2008 @ WWW2008 * Define the scope of the ontology from use cases. Derive essential concepts. Construct concept taxonomy. Map to an upper level ontology Assign relations between concepts and attributes. Add complex class descriptions. METHODOLOGY HCLS2008 @ WWW2008 * 1 SCOPE researcher, doctor or patient personalized medicine What is the most effective drug treatment for an individual with a particular genetic profile that suffers from a particular disease? Which gene variants affec