our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality.

1.8. Asserted monohierarchies Inspired in part by (Rector, 2003), we advocate the following:

Principle of asserted single inheritance. Each reference ontology module should be built as an asserted monohierarchy (a hierarchy in which each term has at most one parent).

This means that the ontology will have a single root node, and that all non-root terms will have exactly one is_a parent and thus be connected by exactly one chain of is_a relations to the root. To say that the is_a relations are asserted means that they are included in the ontology manually by the ontology’s developers and form the basis for the associated definitions.

Terms in the resultant asserted hierarchies can be used in various combinations, using relations taken over from the Relation Ontology (RO) (Smith, 2005) to form new terms, following a methodology first applied in relation to the GO and its sister ontologies in Wroe et al. (2003) (compare also Hill et al., 2002; Mungall, 2004). The goal is both to reduce the degree of arbitrariness typically involved in term composition in ontologies, and to ensure that ontologies are developed in tandem in such a way as to constitute a progressively more well-integrated modular network.4 A term such as blood glucose measurement, for example, is formed from FMA:portion of blood, ChEBI:glucose and OBI:act of measurement. When a classifier is applied to the result of adding such a term, with its definition, to the already existing set of asserted monohierarchies, then certain further is_a relations will be able to be inferred. This will in some cases yield a polyhierarchy, or in other words a hierarchy in which some terms will have more than one is_a parent (hence ‘multiple inheritance’ – meaning that the entities represented by a term with multiple parents will inherit a corresponding set of attributes from each of its parents).

Rector (2003) has developed a methodology for ‘normalizing’ ontologies by decomposing existing polyhierarchies into homogeneous disjoint monohierarchies. For him, the monohierarchies are then recombined using logical definitions from which an enriched poly-hierarchy can be inferred mechanically using a theorem prover or reasoner.

Tue, Feb 16, 2021