Clinical and Translational Science Ontology Workshop

The National Center for Biomedical Ontology will hold a Clinical and Translational Science Ontology Tutorial and Workshop in its series of training and dissemination events.

Venue: Hilton Garden Inn Baltimore Airport

Date:

Tutorial: April 24, 2012

Workshop: April 25-26, 2012

Organization: Barry Smith (NCBO), Jessica Tenenbaum (Duke), Rob Wynden (UCSF)

The Tutorial will provide a beginners' 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 within and beyond the CTSA Consortium to review what has been achieved thus far. It will feature presentations of on-going work on ontology-supported research at CTSA Consortium institutions and conclude with consideration of plans and strategies for enhanced coordination in the future.

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Tutorial (Tuesday, April 24, 10.30am-6pm)

Introduction to Biomedical Ontology for Non-Experts

Foundations of Biomedical Ontology

What is an ontology and what is it useful for?

The problem of data silos

NIH mandates for sharing and reuse of research data

Examples of biomedical ontologies:

• Gene Ontology (GO)
• Foundational Model of Anatomy (FMA)
• Infectious Disease Ontology (IDO)

Ontology Technology

An Introduction to the Semantic Web and the Web Ontology Language (OWL)

Using ontologies for data retrieval, integration and reasoning

Success stories

Basic information on ontology editing tools

Use of Bioportal

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Workshop (Day 1: Wednesday, April 25, 9am-5pm)

Major Ontology Initiatives relevant to Clinical and Translational Research

Chris Chute (Mayo): Data Governance and Normalization within the Mayo Clinic Enterprise

Melissa Haendel (Oregon) and Jon Corson-Rikert (Cornell): eagle-i and VIVO Ontology Initiatives

Jessica Tenenbaum (Duke): Remarks on Genetics Ontologies 

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

Possibly also: OCRe (for clinical research), Permissions Ontology (for consent; owned by Jihad Obeid at Medical University of South Carolina); biobanking ontology (Arkansas)

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Workshop (Day 2: Thursday, April 26, 9am-4pm)

EHR, Ontology and Interoperability

Presentations by EHR vendors

Rob Wynden (UCSF): The Health Ontology Mapper (HOM).

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?

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Participants

Participants will include:

Mathias Brochhausen (University of Arkansas for Medical Sciences)

Alexander Diehl (University at Buffalo)

Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)

Melissa Haendel (Oregon Health Sciences University)

William Hogan (Translational Research Institute, University of Arkansas for Medical Sciences)

Shawn Murphy (Partners Healthcare Research Computing / Harvard Medical School)

Mark Musen (Stanford Center for Biomedical Informatics Research / NCBO)

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)

Jessica Tenenbaum (Duke Translational Medicine Institute)

Rob Wynden (University of California at San Francisco)