This article is part of the supplement: Proceedings of the Bio-Ontologies Special Interest Group Meeting 2010
Proceedings
Scalable representations of diseases in biomedical ontologies
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* Corresponding author: Stefan Schulz stefan.schulz@medunigraz.at
1 Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria
2 International Health Terminology Standards Development Organisation, Copenhagen, Denmark
3 Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
4 Saint Francis Xavier University, Antigonish, Nova Scotia, Canada
5 Institute of Medical Biometry und Medical Informatics, University Medical Center Freiburg, Germany
Journal of Biomedical Semantics 2011, 2(Suppl 2):S6 doi:10.1186/2041-1480-2-S2-S6
Published: 17 May 2011Abstract
Background
The realm of pathological entities can be subdivided into pathological dispositions, pathological processes, and pathological structures. The latter are the bearer of dispositions, which can then be realized by their manifestations — pathologic processes. Despite its ontological soundness, implementing this model via purpose-oriented domain ontologies will likely require considerable effort, both in ontology construction and maintenance, which constitutes a considerable problem for SNOMED CT, presently the largest biomedical ontology.
Results
We describe an ontology design pattern which allows ontologists to make assertions that blur the distinctions between dispositions, processes, and structures until necessary. Based on the domain upper-level ontology BioTop, it permits ascriptions of location and participation in the definition of pathological phenomena even without an ontological commitment to a distinction between these three categories. An analysis of SNOMED CT revealed that numerous classes in the findings/disease hierarchy are ambiguous with respect to process vs. disposition. Here our proposed approach can easily be applied to create unambiguous classes. No ambiguities could be defined regarding the distinction of structure and non-structure classes, but here we have found problematic duplications.
Conclusions
We defend a judicious use of disjunctive, and therefore ambiguous, classes in biomedical ontologies during the process of ontology construction and in the practice of ontology application. The use of these classes is permitted to span across several top-level categories, provided it contributes to ontology simplification and supports the intended reasoning scenarios.