title: The extraction of pharmacogenetic and pharmacogenomic relations--a case study using PharmGKB.
abstract: In this paper, we report on adapting the JREX relation extraction engine, originally developed For the elicitation of protein-protein interaction relations, to the domains of pharmacogenetics and pharmacogenomics. We propose an intrinsic and an extrinsic evaluation scenario which is based on knowledge contained in the PharmGKB knowledge base. Porting JREX yields favorable results in the range of 80% F-score for Gene-Disease, Gene-Drug, and Drug-Disease relations.
authors.affiliation: Jena University Language & Information Engineering (JULIE) Laboratory, Friedrich-Schiller-Universität Jena, Jena, Germany. ekaterina.buyko@uni-jena.de
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Buyko
authors.forename: Elena
authors.initials: E
authors.lastname: Beisswanger
authors.forename: Udo
authors.initials: U
authors.lastname: Hahn
mesh_terms: D001189:Aryl Hydrocarbon Hydroxylases / Q000235:genetics / Q000378:metabolism; D001943:Breast Neoplasms / Q000188:drug therapy / Q000235:genetics; D015283:Citalopram / Q000493:pharmacokinetics; D019295:Computational Biology; D065731:Cytochrome P-450 CYP2C19; D016208:Databases, Factual; D030541:Databases, Genetic; D000077143:Docetaxel; D005260:Female; D024522:Genes, BRCA2; D020022:Genetic Predisposition to Disease; D006801:Humans; D051188:Knowledge Bases; D009765:Obesity / Q000235:genetics; D010597:Pharmacogenetics / Q000592:standards / Q000706:statistics & numerical data*; D010599:Pharmacokinetics; D025941:Protein Interaction Mapping / Q000706:statistics & numerical data; D043823:Taxoids / Q000627:therapeutic use; D054832:Urocortins / Q000235:genetics
chemical_list: D043823:Taxoids; D054832:Urocortins; D015283:Citalopram; D000077143:Docetaxel; D001189:Aryl Hydrocarbon Hydroxylases; C045793:CYP2C19 protein, human; D065731:Cytochrome P-450 CYP2C19