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Appl Ontol 2010 Nov;5(3-4):139-188

New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA.

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. Read More

Appl Ontol 2008 Jan;3(3):173-190

Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, United States, ,

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. Read More