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

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.Research activities in the "omics" sciences yield an ever-growing content of experimental data and publications, which are stored in a large variety of databases. For meta-data descriptions and mediation between these resources a large number of bio-ontologies have evolved. In a similar vein, medical terminology and classification systems have been developed in order to improve medical documentation and data analysis.Whereas naive methods of ontology engineering (typically, the ad-hoc assembly of concept trees and graphs) were prevailing in the past, the claim is increasingly expressed for a more principled approach, based upon logics and formal ontology design methodologies. (We here understand by formal ontologies representational artifacts which use a formal language to describe entities and their relations in the domain of choice.) The need for taming the mass of newly generated domain knowledge requires sophisticated and rigid computational methods to support semantic interoperability on a large scale. This can only be fulfilled when discretionary modeling decisions and implicit semantic assumptions underlying the assembly of terms and relations are avoided, as much as possible.This paper is structured in the following way. First we will address taxonomies and partonomies as the main hierarchical principles in the context of concrete instances of bio-ontologies. We will introduce relations considered canonical to relate entitie