ABSTRACT

BUILDING REASON-ABLE BIOINFORMATICS ONTOLOGIES with DAML+OIL

Dr. Robert Stevens Department of Computer Science, University of Manchester

The biology community is large and distributed, with a tendency for separate domains to plough their own furrows in terms of terminology and conceptualisation. The post-genomic era means that inter-species comparison at the genome level, across huge and complex data sets, are now possible. This scenario, together with the ever- present need to ask complex questions involving many distributed, autonomous and heterogeneous data resources mean that both humans and computers need semantic descriptions of their domain in order to give the shared understanding needed for complex questions to be asked and answered. As a result, there has been growing interest in the use of ontologies in the bioinformatics domain over the past decade.

The talk will describe the nature of biology's resources and why ontologies are needed. It will briefly describe our favoured knowledge representation language, DAML+OIL, and its capabilities. The principal of these are its expressiveness and its reasoning support, which allow sound and complete maintenence of the concept lattice and post co-ordinated use of the resulting ontology. The speaker will talk about some of the problems of modelling the biological domain, before describing the use of DAML+OIL in two bioinformatics modelling projects. The first, the Gene Ontology Next Generation (GONG), takes a well established community-generated, hand-crafted phrase-based ontology and uses DAML+OIL to add rigour and completeness to its representation. GONG demonstrates how the reasoning support on offer with DAML+OIL allows improved management and building of ontologies. the second project, the myGrid Bioinformatics Services Ontology, shows how the reasoning services can allow dynamic, post co-ordinated construction of partial or complete description on the fly. The reasoning service can then be used to place the new description correctly within the lattice of concepts. In myGrid, this DAML-S based description of bioinformatics services is used to describe and retrieve instances of bioinformatics services from a service repository. the ontology, together with the reasoner and the service repository form the basis of a discovery service.

Maintained by rbennett@cs.ucl.ac.uk