Pragmatic Applications of Ontology to Bioinformatics

Date: December 02, 2003 Time: (All day)
Event Type: Lecture

The complexities inherent to modeling bioinformatics domains and in making use of bioinformatics data suggests a role for ontologically-based knowledge management systems, which have shown promise for managing and integrating complex heterogeneous data. Ontologies can do more than serve as expressive representations of accepted biological theory _ they can and should be used as a basis for semantic integration of domain knowledge and as a foundation for application development. Software systems supporting ontologies should facilitate verification and improvement of both the ontology's internal consistency, and consistency between the ontology and overarching ontological principles. Database schemas can be automatically generated from ontologies, and databases should verify data quality (i.e. verifying that data are consistent with the ontology). Sufficiently expressive ontologies and ontological methodology are not only useful for elucidating and representing domain concepts, but also have the beneficial side-effect of allowing advanced reasoning over the ontologies themselves and their resulting databases, facilitating the research process. We use examples from the Gene Ontology and other sources to illustrate some of these tenets of ontological methodology, construction and pragmatic application, and we introduce Ontology Works, a company whose mission is to advance the pragmatic applications of ontology to biomedical informatics and to other areas.