How to Make Useful Ontologies for Biomedicine

 When: July 19, 2008
 Where: ISMB 2008, Toronto, Canada
 What: Tutorial on How to Make Useful Ontologies for Biomedicine

Brief: The tutorial provides an overview of current uses of ontologies in bioinformatics, instruction on ontology development using OWL, and an outline of principles of good ontology design. It comprises an interactive session devoted to developing an ontology, and a session illustrating how good design practices effect the usefulness of ontologies in practice.

Tutorial level: Introductory/Intermediate

Prior knowledge required: Participants should be at least aware of ontologies such as the Gene Ontology. Familiarity with basic biology is required.

Abstract: Ontologies are becoming essential for data integration as a result of the increase in the quantities and types of data in the molecular biology domain. Simultaneously, the need to organise, co-ordinate and disseminate ontologies as well as coherent ontology development methods is now accepted and is evidenced by the funding of the National Center for Biomedical Ontology (NCBO). Though the need to use ontologies is widely appreciated, the right manner in which they should be developed and applied is not well understood. Researchers still resort to ad hoc methods in developing and using ontologies, resulting in lost opportunities for integration and cross-disciplinary communication, and creation of obstacles to cross-domain reasoning. This tutorial will provide an overview of how ontologies are used in bioinformatics and biomedicine including innovative applications of ontologies such as validation of pathway data and cross-database reasoning. It will educate the participants on what ontologies are and how they are currently used in biomedicine. It will draw on ontology development methods discussed in our recent Nature Biotechnology paper. It will provide instruction on how to create ontologies using OWL, on best practices for ontology development, and clarify the relationship between Open Biomedical Ontologies (OBO) and OWL. This tutorial will be aimed at advanced graduate students and researchers who need to understand the basic principles underlying ontology development in order to use ontologies effectively for interpreting (and annotating) their datasets. It will be of value to researchers who participate in ontology development efforts in their respective scientific communities. This tutorial was very well received at ISMB 2007.

Slides are available at: Slides

The handout is available at: Handout