HCLSIG/Use case/TMO for pharmacogenomics

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Use case

Extending the Translational Medicine Ontology (TMO) to cover pharmacogenomics and personalized / stratified medicine

Projected timeframe

November 2011 - February 2012.


Objective

what are we trying to achieve?

The extension of the Translational Medicine Ontology (TMO) in order to support (FDA-approved) pharmacogenomic clinical decision support. The TMO should provide a scaffold by which data from different sources can be integrated in order to i) answer questions regarding the relationship between gene variants, drugs and therapeutic outcomes and ii) provide FDA-approved clinical guidelines for drugs have pharmacogenomic alerts.


Stakeholders Who are the main actors?

  • Ontology Designers - SOPHARM [adrien], PG ontology [michel], Sequence Ontology
  • Schemas - NCI - LS-DAM
  • Data - PharmGKB [russ altman], cancercommons.org
  • Clinical Decisions Support - Mayo Clinic, Cleveland Clinic?
  • Regulatory Agency - FDA, Health Canada

Value Proposition

Does the use case capture current behaviour, improved or novel functionality? What is the significance or impact of having such functionality?

By formalizing the representation of pharmacogenomic knowledge, and making a commitment to it, it becomes possible to query the knowledge base in a consistent manner, and in a way that integrates with other knoweldge regardless of the form of the original data.

SNPs - PGx support can be found in SO-PHARM and PGO, but their representation differs. The TMO would unify these efforts by having a consistent, agreed upon representation.

Other data - TCGA


Methods

What steps would be taken to achieve the task? Compare and contrast with other, related work.

  • Identify use cases
  • Compare and contrast relevant vocabulary
  • Diagram of key entities and relationships
  • Addition of classes and relations to the TMO
  • Identify and create mappings to relevant linked data
  • Demonstrate TMO-based queries over linked data

Components

What components are required to successfully complete the task? Do any of the components already exist? If so, indicate their strengths, weaknesses and availability (free, license, etc)

Deliverables

Describe each component that will be developed along with the expected timeframe and necessary resources - human and otherwise. Examples include:

  • Software: TMO with classes and relationships of relevance to PGx
  • Written: A conference article for ICBO 2012 (International Conference on Biomedical Ontology, http://www.kr-med.org/icbofois2012/). Submission deadline 29. January, 2012.
  • Written: W3C Note

Partners

Identify individuals and organizations that will participate in the project, and the capacity in which they will do so.

  • Matthias Samwald, Medical University of Vienna and University of Technology Vienna, Austria
  • Adrien Coulet, LORIA – INRIA, France
  • Robert R. Freimuth, Mayo Clinic, USA
  • Robert L. Powers, Predictive Medicine, Inc., USA
  • Michel Dumontier, Carleton University
  • Scott Marshall
  • Joanne Luciano, Rensselaer Polytechnic Institute, USA
  • Jyotishman Pathak, Mayo Clinic, USA
  • Please add your name if interested!


Success Criteria

By what criteria will the project success be established? Examples include:

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