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Comparative and Functional Genomics
Volume 6, Issue 7-8, Pages 379-387
Research article

On Carcinomas and Other Pathological Entities

1Ifomis, University of Saarbröcken, Germany
2Department of Philosophy, University at Buffalo and National Center for Biomedical Ontology, 126 Park Hall, Buffalo, NY 14260, USA
3European Centre for Ontological Research, University of Saarbröcken, Germany
4Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA, USA

Received 24 May 2005; Revised 1 October 2005; Accepted 7 November 2005

Copyright © 2005 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Tumours, abscesses, cysts, scars and fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transformation_of can facilitate the integration of such ontologies in ways which have the potential to support new kinds of automated reasoning. We here extend this approach to the treatment of pathologies, focusing especially on those pathological continuant entities which arise when organs become affected by carcinomas.