Affiliations: Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA. E-mails: {noy, musen}@stanford.edu | National Cancer Institute, Center for Biomedical Informatics and Information Technology, Bethesda, MD 20892-8335, USA. E-mails: {decoronos, fragosog, hartel}@mail.nih.gov | Apelon Inc. Ridgefield, CT, USA. E-mail: [email protected]
Note: [] Corresponding author: Natalya F. Noy, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA. E-mail: [email protected].
Abstract: The National Cancer Institute's (NCI) Thesaurus is a biomedical reference ontology. The NCI Thesaurus is represented using description logic, more specifically Ontylog, a description logic implemented by Apelon, Inc. We are exploring the use of the DL species of the Web Ontology Language (OWL DL) – a W3C recommended standard for ontology representation – instead of Ontylog for representing the NCI Thesaurus. We have studied the requirements for knowledge representation of the NCI Thesaurus, and considered how OWL DL (and its implementation in Protégé-OWL) satisfies these requirements. In this paper, we discuss the areas where OWL DL was sufficient for representing required components, where tool support that would hide some of the complexity and extra levels of indirection would be required, and where language expressiveness is not sufficient given the representation requirements. Because many of the knowledge-representation issues that we encountered are very similar to the issues in representing other biomedical terminologies and ontologies in general, we believe that the lessons that we learned and the approaches that we developed will prove useful and informative for other researchers.
