Abstract
BackgroundIn biomedical ontologies, mereological relations have always been subject to special interest due to their high relevance in structural descriptions of anatomical entities, cells, and biomolecules. This paper investigates two important subrelations of has_proper_part, viz. the relation has_grain, which relates a collective entity to its multiply occurring uniform parts (e.g., water molecules in a portion of water), and the relation has_component, which relates a compound to its constituents (e.g., molecules to the atoms they consist of).MethodWe distinguish between four kinds of complex entities and characterize them in first order logic. We then discuss whether similar characterizations could be given in description logics, and finally apply the results to mixtures.ResultsAt first sight, collectives and compounds seem to be disjoint categories. Their disjointness, however, relies on agreement about what are uniform entities, and thus on the granularity of description. For instance, the distinction between isomeric subtypes of a molecule can be important in one use case but might be neglected in another one. We demonstrate that, as implemented in the BioTop domain upper level ontology, equivalence or subsumption between different descriptions of same or similar entities cannot be achieved. Using OWL-DL, we propose a new design pattern that avoids primitive subrelations at the expense of more complex descriptions and thus supports the needed inferences.
Highlights
In biomedical ontologies, mereological relations have always been subject to special interest due to their high relevance in structural descriptions of anatomical entities, cells, and biomolecules
As implemented in the BioTop domain upper level ontology, equivalence or subsumption between different descriptions of same or similar entities cannot be achieved
Using OWL-Description Logics (DL), we propose a new design pattern that avoids primitive subrelations at the expense of more complex descriptions and supports the needed inferences
Summary
Mereological relations have always been subject to special interest due to their high relevance in structural descriptions of anatomical entities, cells, and biomolecules. Mereology in the biomedical domain In biomedical ontologies, mereological relations between parts and wholes [1] have always been conferred a special importance due to their relevance for describing the structural makeup of material entities such as body parts, cells, cell components, and biomolecules ([1,2,3]). Numerous subrelations of the foundational has_part relation, relevant for the biomedical domain, have been proposed in the context of biomedical ontologies such as GALEN [4] or the Foundational Model of Anatomy (FMA) [5]. The need for two distinct mereological relations, has_grain and has_component, both subrelations of has_proper_part, has been advocated. We will first present the approach of BioTop, discuss it critically, and present a new suggestion and discuss whether it can and should be applied to mixtures, too
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