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2014 ; 1159
(ä): 47-75
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English Wikipedia
Text mining for drug-drug interaction
#MMPMID24788261
Wu HY
; Chiang CW
; Li L
Methods Mol Biol
2014[]; 1159
(ä): 47-75
PMID24788261
show ga
In order to understand the mechanisms of drug-drug interaction (DDI), the study
of pharmacokinetics (PK), pharmacodynamics (PD), and pharmacogenetics (PG) data
are significant. In recent years, drug PK parameters, drug interaction
parameters, and PG data have been unevenly collected in different databases and
published extensively in literature. Also the lack of an appropriate PK ontology
and a well-annotated PK corpus, which provide the background knowledge and the
criteria of determining DDI, respectively, lead to the difficulty of developing
DDI text mining tools for PK data collection from the literature and data
integration from multiple databases.To conquer the issues, we constructed a
comprehensive pharmacokinetics ontology. It includes all aspects of in vitro
pharmacokinetics experiments, in vivo pharmacokinetics studies, as well as 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.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.