Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL

Qian Zhu, Robert Freimuth, Jyotishman Pathak, Matthew J. Durski, Christopher G. Chute

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

PharmGKB is a leading resource of high quality pharmacogenomics data that provides information about how genetic variations modulate an individual's response to drugs. PharmGKB contains information about genetic variations, pharmacokinetic and pharmacodynamic pathways, and the effect of variations on drug-related phenotypes. These relationships are represented using very general terms, however, and the precise semantic relationships among drugs, and diseases are not often captured. In this paper we develop a protocol to detect and disambiguate general clinical associations between drugs and diseases using more precise annotation terms from other data sources. PharmGKB provides very detailed clinical associations between genetic variants and drug response, including genotype-specific drug dosing guidelines, and this procedure will armGKB. The availability of more detailed data will help investigators to conduct more precise queries, such as finding particular diseases caused or treated by a specific drug.We first mapped drugs extracted from PharmGKB drug-disease relationships to those in the National Drug File Reference Terminology (NDF-RT) and to Structured Product Labels (SPLs). Specifically, we retrieved drug and disease role relationships describing and defining concepts according to their relationships with other concepts from NDF-RT. We also used the NCBO (National Center for Biomedical Ontology) annotator to annotate disease terms from the free text extracted from five SPL sections (indication, contraindication, ADE, precaution, and warning). Finally, we used the detailed drug and disease relationship information from NDF-RT and the SPLs to annotate and disambiguate the more general PharmGKB drug and disease associations.

Original languageEnglish (US)
Pages (from-to)690-696
Number of pages7
JournalJournal of Biomedical Informatics
Volume46
Issue number4
DOIs
StatePublished - Aug 2013

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Terminology
Labels
Pharmaceutical Preparations
Pharmacodynamics
Pharmacokinetics
Ontology
Biological Ontologies
Semantics
Availability
Network protocols
Information Storage and Retrieval
Pharmacogenetics

Keywords

  • Clinical associations
  • NDF-RT
  • Pharmacogenomics
  • PharmGKB
  • SPL

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

Cite this

Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL. / Zhu, Qian; Freimuth, Robert; Pathak, Jyotishman; Durski, Matthew J.; Chute, Christopher G.

In: Journal of Biomedical Informatics, Vol. 46, No. 4, 08.2013, p. 690-696.

Research output: Contribution to journalArticle

Zhu, Qian ; Freimuth, Robert ; Pathak, Jyotishman ; Durski, Matthew J. ; Chute, Christopher G. / Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL. In: Journal of Biomedical Informatics. 2013 ; Vol. 46, No. 4. pp. 690-696.
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