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

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Citations (Scopus)

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 languageEnglish (US)
Title of host publicationStudies in Health Technology and Informatics
Pages539-542
Number of pages4
Volume192
Edition1-2
DOIs
StatePublished - 2013
Event14th World Congress on Medical and Health Informatics, MEDINFO 2013 - Copenhagen, Denmark
Duration: Aug 20 2013Aug 23 2013

Other

Other14th World Congress on Medical and Health Informatics, MEDINFO 2013
CountryDenmark
CityCopenhagen
Period8/20/138/23/13

Fingerprint

Clinical Decision Support Systems
Knowledge Bases
Pharmacogenetics
Ontology
Genetic Testing
Semantics
Drug therapy
Language
Drug Therapy
Drug products
Information management
Labels
Pharmaceutical Preparations
Testing

Keywords

  • clinical decision support systems
  • medical informatics
  • ontology
  • Pharmacogenetics
  • pharmacogenomics

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Samwald, M., Freimuth, R., Luciano, J. S., Lin, S., Powers, R. L., Marshall, M. S., ... Boyce, R. D. (2013). An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics. In Studies in Health Technology and Informatics (1-2 ed., Vol. 192, pp. 539-542) https://doi.org/10.3233/978-1-61499-289-9-539

An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics. / Samwald, Matthias; Freimuth, Robert; Luciano, Joanne S.; Lin, Simon; Powers, Robert L.; Marshall, M. Scott; Adlassnig, Klaus Peter; Dumontier, Michel; Boyce, Richard D.

Studies in Health Technology and Informatics. Vol. 192 1-2. ed. 2013. p. 539-542.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Samwald, M, Freimuth, R, Luciano, JS, Lin, S, Powers, RL, Marshall, MS, Adlassnig, KP, Dumontier, M & Boyce, RD 2013, An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics. in Studies in Health Technology and Informatics. 1-2 edn, vol. 192, pp. 539-542, 14th World Congress on Medical and Health Informatics, MEDINFO 2013, Copenhagen, Denmark, 8/20/13. https://doi.org/10.3233/978-1-61499-289-9-539
Samwald M, Freimuth R, Luciano JS, Lin S, Powers RL, Marshall MS et al. An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics. In Studies in Health Technology and Informatics. 1-2 ed. Vol. 192. 2013. p. 539-542 https://doi.org/10.3233/978-1-61499-289-9-539
Samwald, Matthias ; Freimuth, Robert ; Luciano, Joanne S. ; Lin, Simon ; Powers, Robert L. ; Marshall, M. Scott ; Adlassnig, Klaus Peter ; Dumontier, Michel ; Boyce, Richard D. / An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics. Studies in Health Technology and Informatics. Vol. 192 1-2. ed. 2013. pp. 539-542
@inproceedings{c37cc3d37587417981c848eec6008729,
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.",
keywords = "clinical decision support systems, medical informatics, ontology, Pharmacogenetics, pharmacogenomics",
author = "Matthias Samwald and Robert Freimuth and Luciano, {Joanne S.} and Simon Lin and Powers, {Robert L.} and Marshall, {M. Scott} and Adlassnig, {Klaus Peter} and Michel Dumontier and Boyce, {Richard D.}",
year = "2013",
doi = "10.3233/978-1-61499-289-9-539",
language = "English (US)",
isbn = "9781614992882",
volume = "192",
pages = "539--542",
booktitle = "Studies in Health Technology and Informatics",
edition = "1-2",

}

TY - GEN

T1 - An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics

AU - Samwald, Matthias

AU - Freimuth, Robert

AU - Luciano, Joanne S.

AU - Lin, Simon

AU - Powers, Robert L.

AU - Marshall, M. Scott

AU - Adlassnig, Klaus Peter

AU - Dumontier, Michel

AU - Boyce, Richard D.

PY - 2013

Y1 - 2013

N2 - 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.

AB - 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.

KW - clinical decision support systems

KW - medical informatics

KW - ontology

KW - Pharmacogenetics

KW - pharmacogenomics

UR - http://www.scopus.com/inward/record.url?scp=84894309334&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84894309334&partnerID=8YFLogxK

U2 - 10.3233/978-1-61499-289-9-539

DO - 10.3233/978-1-61499-289-9-539

M3 - Conference contribution

SN - 9781614992882

VL - 192

SP - 539

EP - 542

BT - Studies in Health Technology and Informatics

ER -