In Achille Varzi Laure Vieu (ed.), ”, Formal Ontology in Information Systems. Proceedings of the Third International Conference. IOS Press. pp. 37–48 (2004)

Barry Smith
State University of New York, Buffalo
Maureen Donnelly
State University of New York, Buffalo
Thomas Bittner
State University of New York, Buffalo
This paper provides an axiomatic formalization of a theory of foundational relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the is-a relation among universals and the part-of relation among individuals as well as cross-category relations such as instance-of, member-of, and partition-of. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for formal ontology. We provide examples to support this thesis from the domain of biomedicine.
Keywords temporal mereology  aggregates  sets vs. collections vs. wholes
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Fiat and Bona Fide Boundaries.Barry Smith & Achille C. Varzi - 2000 - Philosophy and Phenomenological Research 60 (2):401-420.
The Role of Foundational Relations in the Alignment of Biomedical Ontologies.Barry Smith & Cornelius Rosse - 2004 - In M. Fieschi, E. Coiera & Y.-C. J. Li (eds.), Medinfo. IOS Press. pp. 444-448.

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A Spatio-Temporal Ontology for Geographic Information Integration.Thomas Bittner & Barry Smith - 2009 - International Journal for Geographical Information Science 23 (6):765-798.

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