Introduction to Bio-Ontologies and Their Applications

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: Stanford Center for Biomedical Informatics Research, Stanford University

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.

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Agenda:

• 1:00pm What is an ontology and what is it useful for? (Barry Smith)

This section will provide an introduction to biomedical ontology with a focus on illustrations of success stories in the application of ontologies to supporting specific kinds of research.

• 2:30pm NCBO Web Services and Development of Semantic Applications (Trish Whetzel). Overview presentation of NCBO Web services and how they are being incorporated into software applications.
  • Introduction to REST Web services
  • NCBO BioPortal
  • NCBO REST Web services
    • Ontology Web services - Search, Traverse, Download
    • View Extraction Web service - Subset
    • Notes Web service - Propose Terms, Comment
    • Mapping Web services - Create, Upload, Download
    • Widgets - Tree view, Auto-complete, Graph view
    • Annotation - Ontology Term recognition
    • Data Access - Fetch ontology-indexed data
  • BioPortal SPARQL Endpoint - Access Ontologies via SPARQL

• 4:00pm Use of ontologies in biomedical research (Nigam Shah)

Links: http://bioportal.bioontology.org/