The 8th Annual Bio-Ontologies Meeting

The eighth annual Bio-Ontologies meeting was held on 24th June at ISMB 2005 in Detroit. Its principle aim over the years has been to build a community forum that brings together biologists and computer scientists to discuss the development and use of ontologies within the domain of biology. During this time, it has aimed to stimulate discussion about the role of Ontologies and their associated technologies for describing, sharing, analysing and searching knowledge about biological systems. Ontology papers have been appearing in the ISMB proceedings since the conference’s inception. Pioneering work by Peter Karp with EcoCyc [1] demonstrated the use of ontologies as the backbone of knowledge bases. Since the first BioOntologies meeting in 1998, ontologies have an increasing presence in bioinformatics; particularly with the advent of the Gene Ontology [2] that demonstrated the value of supplementing genomic annotation with ontology terms. This meeting, like its predecessors from 1998 onwards, has been dominated by talks about the Gene Ontology. This interest in ontology from the biomedical sciences is intersecting with interest in bio-ontologies and their use from the outside world in the form of the Web community; the Semantic Web vision now being actively promoted as the “next generation” Web makes heavy use of ontological technology; this, in turn, is leading to increasing provision of mature tools and experience, lessening the activation energy for those biologists who wish to develop or use ontologies. In the main ISMB conference, the use of semantic web, or at least its technologies, was a recurrent theme. A recurrent issue in this year’s meeting, highlighted particularly by Mark Musen’s keynote, are the attempts to move bio-ontology development to a more industrial scale (Further information about this talk and others mentioned in this article are available from the Bio-Ontologies Website). Currently, ontology development is often carried out by small groups of individuals, mirroring much of biology before the advent of community wide sequencing efforts. With the large numbers of ontologies currently being produced (see http://obo.sourceforge.net, for examples), orthogonality, maintenance and consistency are all becoming key issues. At the current time, there is a relatively poor understanding of both the best practises which are necessary and the technology which will be required to support these best practices; what, for instance, are the best mechanisms for peer review of ontologies; is