Tutorial: Introduction to Biomedical Ontology for Clinical and Translational Research

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Tutorial: Tuesday, April 24, 9:30am-5:30pm (Schedule)

9:30am Registration and Coffee

10:30am Foundations of Biomedical Ontology (Barry Smith)

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)
  • Ontology for General Medical Science (OGMS)
  • Infectious Disease Ontology (IDO)
  • Mental and Neurological Disease Ontologies

12:00 pm Lunch Break

1:00pm The Ontology Landscape (Barry Smith and Nigam Shah)

The National Center for Biomedical Ontology (NCBO)
The Semantic Web and Linked Open Data
BioPortal SPARQL endpoint
Open Biomedical Ontologies (OBO) and the OBO Foundry
The CTSA Ontology Landscape

2:30pm Refrreshment Break

3:00pm Introduction to NCBO Technology (Nigam Shah)

(1) Web Services and BioPortal
Search service
Term services
Annotator Web Service
(2) Using NCBO Technology in your project
(3) Examples of use of NCBO services for data retrieval, integration and reasoning
Resource Index
Enrichment Analysis and http://www.ncbi.nlm.nih.gov/pubmed/21550421
(5) Examples of CTSA use cases enabled by NCBO technology
Health Ontology Mapper
Importing Ontologies into i2b2 Hive

5:30pm Close

Faculty: Barry Smith (Buffalo / NCBO) and Nigam Shah (Stanford / NCBO)

This tutorial will provide participants with an understanding of how ontologies and terminologies are used in a variety of contexts in clinical and translational research.

By the end of the tutorial, participants will be able to:

  • Understand the biomedical ontology landscape
  • Understand the national infrastructure available for data annotation and knowledge management
  • Learn about NCBO supported Web service workflows for clinical and translational research.

The National Center for Biomedical Ontology (NCBO) offers a range of Web services that allow users to access biomedical terminologies and ontologies, to use ontology terms to create pick lists and lexicons, to identify terms from controlled terminologies and ontologies that can describe and index the contents of online data sets (data annotation), and to recommend particular terminologies and ontologies that would be appropriate for data-annotation tasks. The tutorial will demonstrate the use of NCBO resources to facilitate tasks such as semantic data integration, information retrieval, structured data entry, and knowledge management. We will review example use cases for analyses using disease ontologies and for applying NCBO tools to compute the risk of having a myocardial infarction on taking Vioxx (rofecoxib) for Rheumatoid arthritis.

Tutorial Participants

Joel Amoussou (Focused eHealth Innovations, Columbia, MD)

Douglas Anderson (Smart Content Team, Elsevier)

Sivaram Arabandi (Smart Content Strategy, Elsevier)

Rimma Belenkaya (Albert Einstein College of Medicine / CTSA Research Informatics Core)

Olga Brazhnik (National Center for Advancing Translational Sciences, NIH)


Elaine Collier (National Center for Advancing Translational Sciences, NIH)

Lindsay Cowell (North and Central Texas Clinical and Translational Science Initiative / University of Texas Southwestern Medical Center at Dallas)

Alexander Cox (University at Buffalo)

Alexander Diehl (University at Buffalo)

Sharon Elcombe (Mayo Clinic CTSA)

Michael Ferrante (University of Wisconsin Medical Foundation)

Davera Gabriel (Clinical & Translational Science Center, University of California, Davis)

Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)

Bob Gehrke (Mayo Clinic CTSA)

Adela Grando (University of California at San Diego)

Daniel Harris (University of Kentucky Center for Clinical and Translational Science)

Kathleen Hayden (University of Michigan Health System – Medical Center Information Technology)

Lisa Jackson (University of Arkansas for Medical Sciences)

Mark Jensen (University at Buffalo)

Warren Kibbe (Northwestern University Clinical and Translational Sciences Institute)

Justin Lancaster (BiomedServer, Lebanon NH)

Michael Lin (Mayo Clinic CTSA)

Aenoch Lynn (Duke Biobank, Duke Translational Medicine Institute)

Donald A. McClain (University of Utah Center for Clinical & Translational Science)

Eneida A Mendonça (University of Wisconsin - Madison Institute for Clinical and Translational Research)

Tom Mish (University of Wisconsin, Madison CTSA)

John Mark Ockerbloom (University of Pennsylvania Libraries)

Jessica Peterson (Smart Content Team, Elsevier)

Blake Roessler (Research Innovation, University of Michigan / Michigan Institute for Clinical and Health Research)

Jody Sachs (National Center for Advancing Translational Sciences, NIH)

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)

Titus Karl Ludwig Schleyer (University of Pittsburgh Center for Dental Informatics)

Anne Seymour (Biomedical Library, University of Pennsylvania)

Nigam Shah (Stanford Center for Biomedical Informatics Research / NCBO)

Barry Smith (University at Buffalo / NCBO)

Dagobert Soergel (University at Buffalo)

Nicholas H. Steneck (Research Ethics Program, University of Michigan / Michigan Institute for Clinical and Health Research)

Alisa Surkis (New York University School of Medicine)

Jessica Tenenbaum (Duke Translational Medicine Institute)

Carlo Torniai (Oregon Health & Science University / CTSA Connect)

David Towers (University of Wisconsin Medical Foundation)

Alan VanBiervliet (CTSA Steering Committee Member, NLM Respresentative)

Patricia Whetzel (Stanford University / NCBO)

Xin Zheng (Yeshiva University / Einstein CTSA)