Difference between revisions of "HCLSIG/Pharmacogenomics"

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=== Teleconference ===
=== Teleconference ===
This task force meets on the 1st and 3rd Wednesday at 10:15am EST. Be an active participant and join our next call:
This task force meets on the 1st and 3rd Wednesday at 10:15am EST. Be an active participant and join our next call:
* [[/Meetings/2013-05-01_Conference_Call|Next Meeting]]
* [[/Meetings/2013-05-15_Conference_Call|Next Meeting]]
* [http://www.w3.org/wiki/Category:HCLS_PGX Past Meetings]
* [http://www.w3.org/wiki/Category:HCLS_PGX Past Meetings]

Revision as of 09:55, 15 May 2013

Clinical Pharmacogenomics


Understanding how the genetic makeup of individual patients influences the response to pharmaceuticals is essential to the realization of more effective, personalized pharmacotherapy. However, the integration of drug, genotype and phenotype knowledge in medical information systems and its subsequent use in clinical decision making remains a key challenge. This task force is dedicated to developing a biomedical informatics infrastructure that leverages Semantic Web technologies to capture pharmacogenomic findings in such a way that they can be used to inform medical practitioners regarding approved drugs with pharmacogenomic labels. We suggest that such computational technologies are an essential part of personalized medicine, providing key information for translational medicine and clinical care.

This Task Force is lead by Michel Dumontier and Matthias Samwald.


This task force meets on the 1st and 3rd Wednesday at 10:15am EST. Be an active participant and join our next call:


  • Capture use cases for pharmacogenomic clinical research and medicine
  • Formalize the representation of pharmacogenomics-related information using Semantic Web technologies and ontologies
  • Demonstrate the integration of (genomic) patient data with biomedical resources (SNPs, drugs, genes, trials, treatments, adverse events)
  • Demonstrate a working interface to explore and query pharmacogenomic knowledge
  • Demonstrate how such representations can be used for clinical decision support




  • Knowledge Base
  • Decision Support

Selected Publications

  • M Samwald, KP Adlassnig. „Pharmacogenomics in the pocket of every patient? A prototype based on Quick Response (QR) codes“ JAMIA (to appear)
  • M Samwald, A Coulet, I Huerga, RL Powers, JS Luciano, RR Freimuth, F Whipple, E Pichler, E Prud'hommeaux, M Dumontier, MS Marshall. Semantically enabling pharmacogenomic data for the realization of personalized medicine. Pharmacogenomics. 2012 Jan;13(2):201-12. pubmed
  • M Samwald, H Stenzhorn, M Dumontier, MS Marshall, J Luciano, KP Adlassnig. Towards an interoperable information infrastructure providing decision support for genomic medicine. Stud Health Technol Inform. 2011;169:165-9. pubmed
  • Toward semantic modeling of pharmacogenomic knowledge for clinical and translational decision support. PE Boyce, RD., Freimuth, RR., Romagnoli, KM., Pummer. The 2013 AMIA Summit on Translational Bioinformatics, San Francisco, CA. PubMed Central- Pending. (Summary on SlideShare)


  • An informatics infrastructure for translating pharmacogenomic knowledge into clinical practice. Matthias Samwald, Adrien Coulet, Robert R. Freimuth, Iker Huerga, Joanne S. Luciano, Elgar Pichler, Robert L. Powers, Eric Prud’hommeaux, Frederick Whipple, M. Scott Marshall, Michel Dumontier. AMIA 2012.
  • An Ontology-based Formalism, Knowledge Base and Reasoning System for Clinical Genetics. Samwald, M., Freimuth, R., Powers, R., Luciano, J., Prud’hommeaux, E., Boyce, R., Marshall, M., Dumontier, M. Poster presentation at the 2013 AMIA Summit on Translational Bioinformatics. San Francisco, March, 2013.


  • Adrien Coulet
  • Robert Freimuth
  • Iker Huerga
  • Joanne S. Luciano
  • M. Scott Marshall
  • Elgar Pichler
  • Bob Powers
  • Frederick Whipple
  • Simon Lin
  • Richard D. Boyce