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.
Method and Materials: 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 BIT+Cl (Basic Inclusion Theory for Classes). 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.
Conclusion: 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 is along these lines is required
