An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics

Matthias Samwald*, Robert R. Freimuth, Joanne S. Luciano, Simon M. Lin, Robert L. Powers, M Scott Marshall, Klaus-Peter Adlassnig, Michel Dumontier, Richard D. Boyce

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


Genetic testing for personalizing pharmacotherapy is bound to become an important part of clinical routine. To address associated issues with data management and quality, we are creating a semantic knowledge base for clinical pharmacogenetics. The knowledge base is made up of three components: an expressive ontology formalized in the Web Ontology Language (OWL 2 DL), a Resource Description Framework (RDF) model for capturing detailed results of manual annotation of pharmacogenomic information in drug product labels, and an RDF conversion of relevant biomedical datasets. Our work goes beyond the state of the art in that it makes both automated reasoning as well as query answering as simple as possible, and the reasoning capabilities go beyond the capabilities of previously described ontologies.

Original languageEnglish
Pages (from-to)539-542
Number of pages4
JournalStudies in Health Technology and Informatics
Publication statusPublished - 2013
Externally publishedYes


  • Data Mining
  • Database Management Systems
  • Databases, Genetic
  • Databases, Pharmaceutical
  • Decision Support Systems, Clinical
  • Internet
  • Knowledge Bases
  • Natural Language Processing
  • Pharmacogenetics
  • Systems Integration
  • Vocabulary, Controlled
  • Journal Article
  • Research Support, Non-U.S. Gov't


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