title: An integrated pharmacokinetics ontology and corpus for text mining.
abstract: BACKGROUND
  Drug pharmacokinetics parameters, drug interaction parameters, and pharmacogenetics data have been unevenly collected in different databases and published extensively in the literature. Without appropriate pharmacokinetics ontology and a well annotated pharmacokinetics corpus, it will be difficult to develop text mining tools for pharmacokinetics data collection from the literature and pharmacokinetics data integration from multiple databases.
  
  
  METHODS
  A comprehensive pharmacokinetics ontology was constructed. It can annotate all aspects of in vitro pharmacokinetics experiments and in vivo pharmacokinetics studies. It covers all drug metabolism and transportation enzymes. Using our pharmacokinetics ontology, a PK-corpus was constructed to present four classes of pharmacokinetics abstracts: in vivo pharmacokinetics studies, in vivo pharmacogenetic studies, in vivo drug interaction studies, and in vitro drug interaction studies. A novel hierarchical three level annotation scheme was proposed and implemented to tag key terms, drug interaction sentences, and drug interaction pairs. The utility of the pharmacokinetics ontology was demonstrated by annotating three pharmacokinetics studies; and the utility of the PK-corpus was demonstrated by a drug interaction extraction text mining analysis.
  
  
  CONCLUSIONS
  The pharmacokinetics ontology annotates both in vitro pharmacokinetics experiments and in vivo pharmacokinetics studies. The PK-corpus is a highly valuable resource for the text mining of pharmacokinetics parameters and drug interactions.
authors: Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA.
authors: Heng-Yi
authors: HY
authors: Wu
authors: Shreyas
authors: S
authors: Karnik
authors: Abhinita
authors: A
authors: Subhadarshini
authors: Zhiping
authors: Z
authors: Wang
authors: Santosh
authors: S
authors: Philips
authors: Xu
authors: X
authors: Han
authors: Chienwei
authors: C
authors: Chiang
authors: Lei
authors: L
authors: Liu
authors: Malaz
authors: M
authors: Boustani
authors: Luis M
authors: LM
authors: Rocha
authors: Sara K
authors: SK
authors: Quinney
authors: David
authors: D
authors: Flockhart
authors: Lang
authors: L
authors: Li
mesh_terms: D003577:Cytochrome P-450 Enzyme System / Q000235:genetics; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D004347:Drug Interactions; D007654:Ketoconazole / Q000493:pharmacokinetics; D008874:Midazolam / Q000493:pharmacokinetics; D010599:Pharmacokinetics; D013629:Tamoxifen / Q000493:pharmacokinetics
chemical_list: D013629:Tamoxifen; D003577:Cytochrome P-450 Enzyme System; D008874:Midazolam; D007654:Ketoconazole
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