The Logic of Biological Classification and the Foundations of Biomedical Ontology

In Dag Westerståhl (ed.), Logic, Methodology and Philosophy of Science. Proceedings of the 12th International Conference. King's College Publication. pp. 505-520 (2005)
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Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into hierarchies via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances



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Barry Smith
University at Buffalo

References found in this work

SNAP and SPAN: Towards dynamic spatial ontology.Pierre Grenon & Barry Smith - 2004 - Spatial Cognition and Computation 4 (1):69–103.
Do mountains exist? Towards an ontology of landforms.Barry Smith & David Mark - 2003 - Environment and Planning B (Planning and Design) 30 (3):411–427.
On the logic of natural kinds.Nino Cocchiarella - 1976 - Philosophy of Science 43 (2):202-222.

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