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Open Access Open Badges Research article

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

Stefan Schulz13*, Kornél Markó12 and Udo Hahn2

Author Affiliations

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

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

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

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

Published: 20 April 2007



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


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.


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.