Tutorial: Introduction to Biomedical Ontology for Non-Experts

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April 24, 2012

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.

10:00am Registration and coffee

10:30am Morning Session

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)

12:30 pm Lunch

1:30pm Afternoon Session

Ontology Technology: From the Semantic Web to the NCBO Bioportal
An Introduction to the Semantic Web and the Web Ontology Language (OWL)
Introduction to NCBO Technology
  • Use of Bioportal
Using ontologies for data retrieval, integration and reasoning
Success stories
Basic information on ontology editing tools

6:00pm Close