Spatial location and its relevance for terminological inferences in bio-ontologies

doi:10.1186/1471-2105-8-134

BMC Bioinformatics
Volume 8

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Research article

Spatial location and its relevance for terminological inferences in bio-ontologies

Stefan Schulz¹^,3 , Kornél Markó¹^,2 and Udo Hahn²

¹Medical Informatics Department, Freiburg University Hospital, Freiburg, Germany

²Language and Information Engineering (JULIE) Lab, Jena University, Germany

³Master Program in Health Technology, Pontificial Catholic University of Paraná, Curtiba, Brazil

author email corresponding author email

BMC Bioinformatics 2007, 8:134doi:10.1186/1471-2105-8-134


Published:	20 April 2007

Abstract

Background

An adequate and expressive ontological representation of biological organisms and their parts requires formal reasoning mechanisms for their relations of physical aggregation and containment.

Results

We demonstrate that the proposed formalism allows to deal consistently with "role propagation along non-taxonomic hierarchies", a problem which had repeatedly been identified as an intricate reasoning problem in biomedical ontologies.

Conclusion

The proposed approach seems to be suitable for the redesign of compositional hierarchies in (bio)medical terminology systems which are embedded into the framework of the OBO (Open Biological Ontologies) Relation Ontology and are using knowledge representation languages developed by the Semantic Web community.