The extraction of pharmacogenetic and pharmacogenomic relations--a case study using PharmGKB

Pac Symp Biocomput. 2012;376-87.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aryl Hydrocarbon Hydroxylases / genetics
  • Aryl Hydrocarbon Hydroxylases / metabolism
  • Breast Neoplasms / drug therapy
  • Breast Neoplasms / genetics
  • Citalopram / pharmacokinetics
  • Computational Biology
  • Cytochrome P-450 CYP2C19
  • Databases, Factual
  • Databases, Genetic
  • Docetaxel
  • Female
  • Genes, BRCA2
  • Genetic Predisposition to Disease
  • Humans
  • Knowledge Bases*
  • Obesity / genetics
  • Pharmacogenetics / standards
  • Pharmacogenetics / statistics & numerical data*
  • Pharmacokinetics
  • Protein Interaction Mapping / statistics & numerical data
  • Taxoids / therapeutic use
  • Urocortins / genetics

Substances

  • Taxoids
  • Urocortins
  • Citalopram
  • Docetaxel
  • Aryl Hydrocarbon Hydroxylases
  • CYP2C19 protein, human
  • Cytochrome P-450 CYP2C19