Introduction to Bio-Ontologies and Their Applications

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The National Center for Biomedical Ontology will hold an Introduction and Application of Bio-Ontologies tutorial as part of its series of training and dissemination events.

Venue: Oak Lounge West, 2nd Floor, Tresidder Union, Stanford University, Directions.
Date: Tutorial: March 15, 2012
Organization: Barry Smith (NCBO / Buffalo), Trish Whetzel (NCBO / Stanford University), and Nigam Shah (NCBO / Stanford University)
Registration: Please write to Barry Smith
Audience: Some background in bioinformatics or medical informatics is required. No knowledge of ontology is presupposed.


  • 1:00pm What is an ontology and what is it useful for? (Barry Smith)
  • We will provide an introduction to biomedical ontology with a focus on the conditions for successful development and application of ontologies. Topics to be covered include:
    • The reasons for the success of the Gene Ontology (GO)
    • What is the difference between an ontology and a database?
    • Why you should use an ontology to support your research
  • 2:20pm Break
  • 2:30pm Examples of using ontologies in biomedical research (Nigam Shah)
    • We will review the use of NCBO components to create an annotation workflow (specifically using the Annotator and Lexicon Builder components). We will then discuss the applications of this workflow to 9.5 million clinical documents--from the electronic health records of approximately one million adult patients from the STRIDE Clinical Data Warehouse, part of Stanford's CTSA Informatics platform--to identify statistically significant patterns of drug use and to conduct drug safety surveillance.
    • We will discuss how drug–disease co-occurrences and the temporal ordering of drugs and disease mentions in clinical notes can be examined for statistical enrichment and used to detect potential adverse events.
    • We will discuss how analysis such as GO enrichment analysis can be done using other ontologies, such as the Human Disease ontology, and generate biological insights.
  • 3:30pm Break