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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.

Patients are prescribed the same thing but are different.jpg

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


Teleconferences are held when needed. Default teleconferene slots are the 1st and 3rd Wednesday of each month at 10:15am EST.


  • 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


Schedule / Milestones

Until October 1, 2014 (to be done)

  • Matthias Samwald
    • Publish commentary paper written by the community in a high-impact journal geared towards medical professionals (e.g. BMJ)
    • Extended consortium of http://safety-code.org/persons.html to include a sizable number of stakeholders in the US and Europe (need to find more European partners)
    • Proposal for Horizon 2020 funding
  • Richard Boyce
  • Michel Dumontier
  • Bob Freimuth
  • Simon Lin
  • others (please add)

Until July 1, 2014 (to be done)

  • Matthias Samwald
    • Submitted the two papers about pre-emptive pharmacogenomic testing and CDSS.
    • First user evaluation results.
  • Richard Boyce
  • Michel Dumontier
  • Bob Freimuth
  • Simon Lin
  • others (please add)

Until March 1, 2014

  • Matthias Samwald
    • Submit paper with analysis of guidelines, assays and regulatory framework for pre-emptive pharmacogenetics to the journal "Pharmacogenomics". IN PROGRESS - SCOPE WAS EXTENDED, MIGHT TAKE 1-3 extra months
    • Genomic CDS ontology covers everything it needs to cover - IN PROGRESS (99% is covered, copy number variants are still lacking, but still needs to be validated. Also, how to formulated CDS messages starts becoming an issue of interest)
    • connection to Rich's annotation work is continuously kept up-to-date -- UNCLEAR STATUS (We need to look at this once again, the last time we tried querying both resources via single SPARQL query did not work too well)
    • Begin partnering with external organizations (clinics, doctors, pharmacies, pharmaceutical companies) to start evaluating and dissemminating the ontology and decision support solutions (as pure research project only, since it is still undecided how best to get the software certified as a medical device). Marshfield Clinic might be a good partnering organisation for pilot studies? -- DONE - but of coure not finished. Starting pilot evaluation with pharmacists in Pittsburgh
  • Richard Boyce
    • Demonstration integration of triggers and recommendations present in the Genomic CDS ontology within the UPMC system using Quest lab results and focused meds (e.g., warfarin, clopidogrel, and some psych drugs). Further qualitative inquiry. - IN PROGRESS
    • Submission of a journal article describing the results from all above research activities. - IN PROGRESS
    • Submission of a journal paper presenting an analysis of pharmgx statements in product including the range of content, frequency of updates, contrasts with other sources, and recommendations for clinicians, drug information compendia, and the FDA - IN PROGRESS
  • Michel Dumontier
    • Identify putative animal models for pharmacogenomic outcomes
  • Bob Freimuth
    • Consider application of gene-drug class and gene-drug-drug rules (leverages drug-drug interaction data)

Until December 1, 2013

  • Matthias Samwald
    • Finalize overhaul and update of Genomic CDS ontology - ONGOING
    • Need to establish more official collaboration with PharmGKB (Michel moving to Stanford might facilitate that further) - ??
    • More official collaboration with the group at Mayo Clinic (Bob Freimuth?) - ??
    • Finalize grant application for additional medical postdoc position -- for someone working on the biomedical details / curation / working and evaluating with doctors - DONE
    • Enable loading VCF files into Genomic CDS - based decision support service. -- ONGOING
  • Richard Boyce
    • Qualitative and possibly quantitative (e.g., task-oriented usability comparison) data on the value of integrating the semantic annotations into a prototype clinical pharmacogenomic information system. ONGOING
    • Acquisition of pilot funding (~25K) for development ONGOING
    • a conference paper describing the above research activities IN PROGRESS
  • Michel Dumontier
    • Be settled at Stanford University DONE
    • Link drug-drug interactions with pharmacogenomic interactions - ??
    • Identify and develop priority datasets to be included in Bio2RDF that would benefit this task force NEEDS DISCUSSION
    • Build relationships with associated partners on RDF data publication, use and analysis ONGOING
  • Bob Freimuth
    • Apply ontological genomic CDS approach to key CPIC guidelines (demonstration, evaluation) -- mostly done by Matthias et al. by now?
    • Demonstrate gene-gene-drug CDS, ensure approach will scale - ??

Until September 1, 2013

  • Matthias Samwald
    • Paper and presentation at OWL Reasoner workshop - DONE
    • Have post-doc in Vienna working on the project full-time - DONE
    • Finalize re-implementation of decision support service (behind http://safety-code.org/) in TrOWL. Need to establish collaboration with Jeff Pan and his group. - DONE
    • Submit paper about Genomic CDS to the journal Bioinformatics - DONE
    • Tidy up / reorganize the W3C wiki - DONE
    • Tidy up / reorganize http://www.genomic-cds.org/ - OVERDUE
  • Richard Boyce
    • Semantically annotated product label information clinical pharmacogenomics statements published as valid Open Data Annotation and with best practice provenance (including IAA) DONE (NOTE:for a sub-set of biomarkers/drugs http://www.youtube.com/watch?v=Te546vOiruo, continuing the project)
  • Michel Dumontier
    • Describe work done this past term with curating class-level drug-drug interactions
      • poster of curated interactions from drugbank; Honors Thesis Student Holly Surins (DONE)
    • Curate and validate annotations for drug effects, drug indications and drug-drug indications on drug product labels (with Rich)
      • installing DOMEO (DONE - Rich)
    • Identify and develop priority datasets to be included in Bio2RDF that would benefit this task force
      • rxnorm
      • stitch
      • clinvar
  • Bob Freimuth
    • Review Cerner's CBO (strengths/gaps for CDS) - ONGOING (had a look at it together with Matthias during Medinfo, Matthias to write down some impressions - a shared Google doc should be started)
    • Discuss modeling approaches for genomic CDS (what's the trigger? integration with/maintenance of knowledge base; review existing implementations (TPP); feedback to CPIC?)
    • Discuss generalization of med safety code approach to NGS of PGx genes - DONE
    • Apply generalized MSC to a real data set (demonstration)
    • Consider opportunities to partner with eMERGE and/or PGRN (user base for generalized MSC) - ONGOING
  • Simon Lin
    • Shape a scientific manuscript out of the use-case document draft at docs.google.com/document/d/12leHdI-GT2dzRgvVIx13wsXAaCLj6eNGvQ-L2B749f4/edit



Selected publications and presentations

  • M Samwald. „Semantically Enabling Genetic Medicine to Facilitate Patients and Guidelines Matching and Enhanced Clinical Decision Support“ Proceedings of the Conference on Semantics in Healthcare and Life Sciences 2013 (CSHALS 2013), February 28, 2013, Cambridge/Boston, Massachusetts, USA - Slides
  • M Samwald, KP Adlassnig. „Pharmacogenomics in the pocket of every patient? A prototype based on Quick Response (QR) codes“ J Am Med Inform Assoc, Published Online First: 23 Jan 2013, http://dx.doi.org/10.1136/amiajnl-2012-001275 - Link to openly accessible preprint version
  • 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.
  • 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)
  • 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
  • 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.
  • 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