The Unified Medical Language System and the Gene Ontology: Some critical reflections

In A. Günter, R. Kruse & B. Neumann (eds.), KI 2003: Advances in Artificial Intelligence. Berlin: Springer. pp. 135-148 (2003)
Authors
Barry Smith
State University of New York, Buffalo
Abstract
The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from the context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications.
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