title: Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL.
abstract: The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge about techniques and best practice on ontology development. In the bio-ontology domain, these two camps have often come into conflict, especially where pragmatism comes into conflict with perceived best practice. One of these areas is the insistence of computer scientists on a well-defined semantic basis for the Knowledge Representation language being used. In this article, we will first describe why this community is so insistent. Second, we will illustrate this by examining the semantics of the Web Ontology Language and the semantics placed on the Directed Acyclic Graph as used by the Gene Ontology. Finally we will reconcile the two representations, including the broader Open Biomedical Ontologies format. The ability to exchange between the two representations means that we can capitalise on the features of both languages. Such utility can only arise by the understanding of the semantics of the languages being used. By this illustration of the usefulness of a clear, well-defined language semantics, we wish to promote a wider understanding of the computer science perspective amongst potential users within the biological community.
authors.affiliation: School of Computer Science, University of Manchester, Manchester, UK. mikel.eganaaranguren@cs.man.ac.uk <mikel.eganaaranguren@cs.man.ac.uk>
authors.forename: Mikel Egaña
authors.initials: ME
authors.lastname: Aranguren
authors.forename: Sean
authors.initials: S
authors.lastname: Bechhofer
authors.forename: Phillip
authors.initials: P
authors.lastname: Lord
authors.forename: Ulrike
authors.initials: U
authors.lastname: Sattler
authors.forename: Robert
authors.initials: R
authors.lastname: Stevens
mesh_terms: D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods; D003628:Database Management Systems; D030541:Databases, Genetic; D005796:Genes; D016247:Information Storage and Retrieval / Q000379:methods*; D009323:Natural Language Processing; D010802:Phylogeny; D011381:Programming Languages; D011506:Proteins / Q000145:classification*; D014584:User-Computer Interface
chemical_list: D011506:Proteins