A Method for Evaluating and Standardizing Ontologies

For my thesis work I am developing a method for evaluating and standardizing ontologies based on an integration of the Basic Formal Ontology (BFO) and OntoClean. BFO serves as the upper ontology for the domain ontologies of the Open Biomedical Ontologies (OBO) Foundry1. The OBO Foundry initiative is a collaborative effort for developing interoperable, science-based ontologies. OntoClean is an approach for the quality assurance of ontologies, and helps a modeler detect when the subsumption relation is used improperly. Ontologies developed for OBO use include some that have been ratified, and others holding the status of “candidate”. To maintain consistency between ontologies, it is important to establish formal principled criteria that a candidate ontology must meet for ratification. The formalisms that result from our integration will serve as criteria an OBO Foundry candidate ontology must satisfy in order to be ratified. The formalisms will also serve as a constraints within a prototype of an ontology editor that interactively asks a modeler questions that helps alleviate constraint violations. The first step in the integration is the unification of the categorical units of OntoClean and BFO. OntoClean uses properties, which are the intension of general terms. BFO uses types, “generalizations about the structure, order, and regularity that exists in nature that experiments and observations make possible” [Spear, 2007, p.16]. We unify property and type under the categorical unit class, since each has a corresponding class. member of(x,A,t) means that the object x satisfies the definition of class A at t. exists at(x,t) means that under a certain ontological theory, object x is within its domain, and it’s existence spans t. OntoClean requires that a modeler characterize their properties with respect to the notions of Identity, Unity, and Rigidity.2 Identity holds for properties for which there is a way to uniquely identify its instances. Unity holds for properties for which their instances are integral wholes. Rigidity is a notion that characterizes a property as either: Rigid, essential to all its instances; Non-Rigid, non-essential to some instance; or Anti-Rigid, non-essential to all instances. In what follows we describe the completed work on integrating the Rigidity