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To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of(More)
We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of(More)
We propose a modular formal ontology of the biomedical domain with two components, one for biological objects, corresponding broadly to anatomy, and one for biological processes, corresponding broadly to physiology. The result constitutes what might be described as a joint venture between two perspectives--of so-called three-dimensionalism and(More)
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF,(More)
There is an assumption commonly embraced by ontological engineers, an assumption which has its roots in the discipline of knowledge representation, to the effect that it is concepts which form the subject-matter of ontology. The term 'con-cept' is hereby rarely precisely defined, and the intended role of concepts within on-tology is itself subject to a(More)
There is a basic distinction, in the realm of spatial boundaries, between bona fide boundaries on the one hand, and fiat boundaries on the other. The former are just the physical boundaries of old. The latter are exemplified especially by boundaries induced through human demarcation, for example in the geographic domain. The classical problems connected(More)
Numerous research groups are now utilizing Basic Formal Ontology (BFO) as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three BFO categories of function, role, and disposition, and considers two proposed sub-categories of artifactual function and biological function.(More)
The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that(More)
Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of(More)