title: A formal theory for spatial representation and reasoning in biomedical ontologies.
abstract: OBJECTIVE
  The objective of this paper is to demonstrate how a formal spatial theory can be used as an important tool for disambiguating the spatial information embodied in biomedical ontologies and for enhancing their automatic reasoning capabilities.
  
  
  METHODS
  This paper presents a formal theory of parthood and location relations among individuals, called Basic Inclusion Theory (BIT). Since biomedical ontologies are comprised of assertions about classes of individuals (rather than assertions about individuals), we define parthood and location relations among classes in the extended theory Basic Inclusion Theory for Classes (BIT+Cl). We then demonstrate the usefulness of this formal theory for making the logical structure of spatial information more precise in two ontologies concerned with human anatomy: the Foundational Model of Anatomy (FMA) and GALEN.
  
  
  RESULTS
  We find that in both the FMA and GALEN, class-level spatial relations with different logical properties are not always explicitly distinguished. As a result, the spatial information included in these biomedical ontologies is often ambiguous and the possibilities for implementing consistent automatic reasoning within or across ontologies are limited.
  
  
  CONCLUSIONS
  Precise formal characterizations of all spatial relations assumed by a biomedical ontology are necessary to ensure that the information embodied in the ontology can be fully and coherently utilized in a computational environment. This paper can be seen as an important beginning step toward achieving this goal, but much more work along these lines is required.
authors.affiliation: Department of Philosophy, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 135 Park Hall, Buffalo, NY 14260, USA. md63@buffalo.edu
authors.forename: Maureen
authors.initials: M
authors.lastname: Donnelly
authors.forename: Thomas
authors.initials: T
authors.lastname: Bittner
authors.forename: Cornelius
authors.initials: C
authors.lastname: Rosse
mesh_terms: D000715:Anatomy / Q000145:classification*; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D048088:Informatics; D008128:Logic; D018875:Vocabulary, Controlled