Representing Natural Kinds by Spatial Inclusion and Containment

Biomedical terminologies lack a clear-cut understanding of the semantics of part-whole relations. In order to design a conceptually adequate ontology for the biomedical domain, we investigate different forms of ontological dependencies between parts and wholes. We then suggest, for natural kinds at least, a move away from modeling the relations between parts and wholes and advocate instead conceptually simpler though expressive spatial inclusion/containment relations. We outline a multi-facetted encoding pattern for biological concepts, which is centered around these relations.