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

doi:10.3233/978-1-61499-289-9-539

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 journal › Article › Academic › peer-review

Abstract

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 language	English
Pages (from-to)	539-542
Number of pages	4
Journal	Studies in Health Technology and Informatics
Volume	192
DOIs	https://doi.org/10.3233/978-1-61499-289-9-539
Publication status	Published - 2013
Externally published	Yes

Keywords

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

Access to Document

10.3233/978-1-61499-289-9-539Licence: CC BY-NC

Cite this

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title = "An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics",

abstract = "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.",

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author = "Matthias Samwald and Freimuth, {Robert R.} and Luciano, {Joanne S.} and Lin, {Simon M.} and Powers, {Robert L.} and Marshall, {M Scott} and Klaus-Peter Adlassnig and Michel Dumontier and Boyce, {Richard D.}",

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AU - Samwald, Matthias

AU - Freimuth, Robert R.

AU - Luciano, Joanne S.

AU - Lin, Simon M.

AU - Powers, Robert L.

AU - Marshall, M Scott

AU - Adlassnig, Klaus-Peter

AU - Dumontier, Michel

AU - Boyce, Richard D.

PY - 2013

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KW - Database Management Systems

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KW - Pharmacogenetics

KW - Systems Integration

KW - Vocabulary, Controlled

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

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