Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL

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 bioontology 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...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Mikel Egaña Aranguren, Sean Bechhofer, Phillip W. Lord, Ulrike Sattler, Robert D. Stevens
• Keywords: BMCBI 2007, Ontology, Semantics, Web Ontology Language