Clinical and Translational Science Ontology Workshop
- Tutorial: April 24, 2012
- Workshop: April 25-26, 2012
Organization: Barry Smith (NCBO / Buffalo), Jessica Tenenbaum (Duke), Rob Wynden (UCSF)
Registration: Please write to Barry Smith
The Tutorial will provide an introduction to ontology methods and technology for students and researchers. Topics highlighted in the tutorial will be of particular interest to individuals at institutions conducting clinical and translational research, including institutions which have or are interested in obtaining CTSA (Clinical and Translational Science Award) grants.
The Workshop will provide an opportunity for those involved in ontology-related projects in the field of clinical and translational science to present on-going work and to review what has been achieved thus far. It will conclude with consideration of plans and strategies for enhanced coordination of ontology development initiatives in the field of clinical and translational science in the future.
Tutorial (Tuesday, April 24, 10.30am-6pm)
An Introduction to Biomedical Ontology for Clinical and Translational Research
- Part I: Foundations of Biomedical Ontology
- Part II: Ontology Technology: From the Semantic Web to the NCBO Bioportal
See schedule here
Workshop Day 1: Wednesday, April 25, 9am-5pm (Draft Schedule)
- Major Ontology Initiatives relevant to Clinical and Translational Research
- Chris Chute (Mayo): Data Governance and Normalization within the Mayo Clinic Enterprise
- The principles and practice of data governance, as undertaken across the Mayo Clinic enterprise, will be reviewed and discussed, with particular emphasis on vocabulary harmonization and practice using NCBO tools for research. Extension to larger-scale consortia including the ONC HIT Standards Committee,SHARPn, ISO, and CIMI will be considered.
- Joseph M. Gunnels and Jihad S. Obeid (Medical University of South Carolina): An Ontology for Informed Consents and Other Research Permissions
- Melissa Haendel (Oregon) and Jon Corson-Rikert (Cornell): VIVO and eagle-i Ontology Initiatives
- VIVO is a platform for managing researcher profiles at or across institutions in support of research expertise location. eagle-i is a system for researchers to share and search for research resources. Both VIVO and eagle-i are ontology-driven, and thereby enable publication of Linked Open Data and complex queries regarding expertise and funding outcomes in the translational science domain. We describe how VIVO and eagle-i ontologies reuse domain standard ontologies for maximum interoperability, and show how they are being used by software applications in the context of the CTSAs.
- Jessica Tenenbaum (Duke): Ontologies for Omic-Scale Datasets
- Harold Lehmann (Baltimore): The Human Studies Database (HSDB) and the Ontology of Clinical Research (OCRe)
- William Hogan (Arkansas) and Werner Ceusters (Buffalo): Referent Tracking and Demographic Data Ontology
- Shawn Murphy (Partners): i2b2-Specific Ontologies
- Richard Scheuermann and Lindsay Cowell (Dallas): NLP-Based Mapping of Textbook Pathology to Ontology for General Medical Science (OGMS)
- Nigam Shah (Stanford): Making Sense of Unstructured Data in Medicine using Ontologies: An Overview of NCBO Technology
Workshop Day 2: Thursday, April 26, 9am-4pm (Draft Schedule)
- 9:00am EHR, Ontology and Interoperability
- Rob Wynden (UCSF): The CTSA Health Ontology Mapper (HOM).
- 12:00pm Lunch
- 1:00pm Next Steps
- How can we measure the value brought by ontology-based approaches?
- How can we ensure high-quality and high-value approaches?
- How can we promote a consistent approach across the CTSA consortium?
Theodora Bakker (New York University Langone Medical Center)
Olga Brazhnik (National Center for Advancing Translational Sciences, NIH)
Mathias Brochhausen (Translational Research Institute, University of Arkansas for Medical Sciences)
Chris Chute (Mayo / NCBO)
Elaine Collier (National Center for Advancing Translational Sciences, NIH)
Alexander Diehl (University at Buffalo)
Michael Ferrante (University of Wisconsin Medical Foundation)
Davera Gabriel (Clinical & Translational Science Center, University of California, Davis)
Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)
Joseph M. Gunnels (Medical University of South Carolina)
Melissa Haendel (Oregon Health & Science University)
Karen Hanson (New York University Langone Medical Center)
William Hogan (Translational Research Institute, University of Arkansas for Medical Sciences)
Pathak Jyotishman (Mayo)
Harold Lehmann (Johns Hopkins / Institute for Clinical and Translational Research
Donald A. McClain (University of Utah Center for Clinical & Translational Science)
Shawn Murphy (Partners Healthcare Research Computing / Harvard Medical School)
Mark Musen (Stanford Center for Biomedical Informatics Research / NCBO)
Michael Sayre (National Institute on Minority Health and Health Disparities, NIH)
Richard Scheuermann (North and Central Texas Clinical and Translational Science Initiative / University of Texas Southwestern Medical Center at Dallas)
Nigam Shah (Stanford Center for Biomedical Informatics Research / NCBO)
Barry Smith (University at Buffalo / NCBO)
Dagobert Soergel (University at Buffalo)
David Stack (University of Wisconsin-Milwaukee)
Alisa Surkis (New York University School of Medicine)
Umberto Tachinardi (University of Wisconsin Medical Foundation)
Jessica Tenenbaum (Duke Translational Medicine Institute)
David Towers (University of Wisconsin Medical Foundation)
Rob Wynden (University of California at San Francisco)