Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL |
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Authors: | Mikel Egaña Aranguren Sean Bechhofer Phillip Lord Ulrike Sattler Robert Stevens |
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Institution: | (1) School of Computer Science, University of Manchester, Manchester, UK;(2) School of Computing Science, University of Newcastle, Newcastle, UK |
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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. |
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