Monday, 5/21/2007
1:15 PM - 4:45 PM
Level: Technical - Intermediate

The Semantic Web has garnered a lot of attention in the Life Sciences community. Among the leading efforts in the field is BioPAX, which is a collaborative effort to create a data exchange format for biological pathway data and is created using the Web Ontology Language (OWL). Protégé OWL is an open source tool created to support ontology development for the Semantic Web. Protégé OWL allows users to edit ontologies in OWL and to use description logic classifiers to maintain consistency of their ontologies. In this introductory tutorial, we will first demonstrate the fundamental features of Protégé OWL to help users develop and manage OWL ontologies. We will also show how to use automatic classification to help content authors create robust ontologies. We will then demonstrate how BioPAX enables the semantic integration of pathway data across diverse resources and show how OWL and other Semantic Web technologies, such as SPARQL, enable rich querying of the integrated pathway resource. At the conclusion of this tutorial, participants will understand some of the capabilities of OWL for semantic web applications in the life sciences and how to get started using OWL.

Daniel Rubin is a Research Scientist at the Stanford Medical Informatics Laboratory, and Clinical Assistant Professor of Radiology at Stanford University. He is Scientific Director of the National Center for Biomedical Ontology and a member of the Protégé group. His research centers on using ontologies to enable intelligent computer applications in radiology and biomedicine.

Nigam Shah is a postdoctoral fellow with the National Center for Biomedical Ontology. He received his MBBS degree from M.S. University in India followed by a PhD in Integrative Biosciences from Penn State University. His thesis work was focused on developing formal methods for the representation, manipulation and integration of diverse biological data - such as gene expression, protein interactions & annotations - with prior biological knowledge for the purpose of evaluating alternative hypotheses. The prototype system is available at www.hybrow.org.

He has conducted tutorials on 'How to make and use ontologies in biomedicine' and lectures on the 'Uses of ontologies' in BMI courses at Stanford. His current research is focused on developing ontology-based reasoning applications in the biomedical sciences.