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Bioinformatics Advance Access originally published online on April 26, 2007
Bioinformatics 2007 23(13):1674-1682; doi:10.1093/bioinformatics/btm155
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

The qualitative and time-dependent character of spatial relations in biomedical ontologies

Thomas Bittner 1,3,* and Louis J. Goldberg 2,3

1Departments of Philosophy and Geography, 2Departments of Oral Biology and Oral Diagnostic Sciences, School of Dental Medicine and 3New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: The formal representation of mereological aspects of canonical anatomy (parthood relations) is relatively well understood. The formal representation of other aspects of canonical anatomy, such as connectedness and adjacency relations between anatomical parts, their shape and size as well as the spatial arrangement of anatomical parts within larger anatomical structures are, however, much less well understood and represented in existing computational anatomical and bio-medical ontologies only insufficiently.

Results: In this article, we provide a methodology of how to incorporate this kind of information into anatomical and bio-medical ontologies by applying techniques of representing qualitative spatial information from Artificial Intelligence. In particular, we focus on how to explicitly take into account the qualitative and time-dependent character of these relations. As a running example, we use the human temporomandibular joint (TMJ).

Availability: Using the presented methodology, a formal ontology was developed which is accessible on http://www.ifomis.org/bfo/fol. This ontology may help to improve the logical and ontological rigor of bio-medical ontologies such as the OBO relation ontology.

Contact: bittner3{at}buffalo.edu

Associate Editor: Alex Bateman

Received on December 14, 2006; revised on April 8, 2007; accepted on April 17, 2007

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