Introduction to Bio-Ontologies and Their Applications
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- 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)
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)