title: Ontology development for a pharmacogenetics knowledge base.
abstract: Research directed toward discovering how genetic factors influence a patient's response to drugs requires coordination of data produced from laboratory experiments, computational methods, and clinical studies. A public repository of pharmacogenetic data should accelerate progress in the field of pharmacogenetics by organizing and disseminating public datasets. We are developing a pharmacogenetics knowledge base (PharmGKB) to support the storage and retrieval of both experimental data and conceptual knowledge. PharmGKB is an Internet-based resource that integrates complex biological, pharmacological, and clinical data in such a way that researchers can submit their data and users can retrieve information to investigate genotype-phenotype correlations. Successful management of the names, meaning, and organization of concepts used within the system is crucial. We have selected a frame-based knowledge-representation system for development of an ontology of concepts and relationships that represent the domain and that permit storage of experimental data. Preliminary experience shows that the ontology we have developed for gene-sequence data allows us to accept, store, and query data submissions.
authors.affiliation: Stanford Medical Informatics, Stanford University School of Medicine, 251 Campus Drive, MSOB X-215, Stanford, CA 94305-5479, USA. oliver@smi.stanford.edu
authors.forename: Diane E
authors.initials: DE
authors.lastname: Oliver
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Rubin
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Stuart
authors.forename: Micheal
authors.initials: M
authors.lastname: Hewett
authors.forename: Teri E
authors.initials: TE
authors.lastname: Klein
authors.forename: Russ B
authors.initials: RB
authors.lastname: Altman
mesh_terms: D000970:Antineoplastic Agents / Q000145:classification / Q000627:therapeutic use; D002352:Carrier Proteins / Q000235:genetics; D016208:Databases, Factual; D004358:Drug Therapy; D004798:Enzymes / Q000235:genetics / Q000378:metabolism; D006801:Humans; D020407:Internet; D010597:Pharmacogenetics / Q000379:methods*
chemical_list: D000970:Antineoplastic Agents; D002352:Carrier Proteins; D004798:Enzymes