Publications

Barry Smith	Ontology and Information Systems Ontology as a branch of philosophy is the science of what is, of the kinds and structures of the objects, properties and relations in every area of reality. 'Ontology' in this sense is often used in such a way as to be synonymous with 'metaphysics'. In simple terms it seeks the classification of entities. Each scientific field will of course have its own preferred ontology, defined by the field's vocabulary and by the canonical formulations of its theories. Traditional (philosophical) ontologists have tended to model themselves on these scientific ontologies, either by producing theories which are like scientific theories but radically more general than these, or by producing theories which represent a regimentation of scientific theories or a clarification of their foundations. Philosophical ontologists have more recently begun to concern themselves not only with the world as this is studied by the sciences, but also with domains of practical activity such as law, medicine, engineering, commerce. They seek to apply the tools of philosophical ontology in order to solve problems which arise in these domains. In the field of information processing there arises what we might call the Tower of Babel problem. Different groups of data-gatherers have their own idiosyncratic terms and concepts in terms of which they represent the information they receive. When the attempt is made to put this information together, methods must be found to resolve terminological and conceptual incompatibilities. Initially, such incompatibilities were resolved on a case-by-case basis. Gradually, however, it was realized that the provision, once and for all, of a common backbone taxonomy of relevant entities of an application domain would provide significant advantages over the case-by-case resolution of incompatibilities. This common backbone taxonomy is referred to by information scientists as an 'ontology'. What is the relationship between these two uses of this term?
Barry Smith	Beyond Concepts: Ontology as Reality Representation 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 ‘concept’ is hereby rarely precisely defined, and the intended role of concepts within ontology is itself subject to a variety of conflicting (and sometimes intrinsically incoherent) interpretations. It seems, however, to be widely accepted that concepts are in some sense the products of human cognition. The present essay is devoted to the application of ontology in support of research in the natural sciences. It defends the thesis that ontologies developed for such purposes should be understood as having as their subject matter, not concepts, but rather the universals and particulars which exist in reality and are captured in scientific laws. We outline the benefits of a view along these lines by showing how it yields rigorous formal definitions of the foundational relations used in many influential ontologies, illustrating our results	In: Achille Varzi and Laure Vieu (eds.), Proceedings of FOIS 2004. InternationalConference on Formal Ontology and Information Systems, Turin, 4-6 November 2004.
Barry Smith Pierre Grenon	The Cornucopia of Formal-Ontological Relations The paper presents a new method for generating typologies of formal ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between three- and four-dimensionalism.	forthcoming in DIALECTICA
Thomas Bittner Maureen Donnelly Barry Smith	Individuals, Universals, Collections: On the Foundational Relations of Ontology 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.	In: Achille Varzi and Laure Vieu (eds.), Proceedings of FOIS 2004. InternationalConference on Formal Ontology and Information Systems, Turin, 4-6 November 2004.
Barry Smith	The Logic of Biological Classification and the Foundations of Biomedical Ontology Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into hierarchies via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances.	Dag Westerståhl (ed.), Invited Papers from the 10th International Conference in Logic Methodology and Philosophy of Science, Oviedo, Spain, 2003 (Elsevier-North-Holland, 2004)
Olivier Bodenreider Barry Smith A. Burgun	The Ontology-Epistemology Divide: A Case Study in Medical Terminology Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain. We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies.	In: Achille Varzi and Laure Vieu (eds.), Proceedings of FOIS 2004. InternationalConference on Formal Ontology and Information Systems, Turin, 4-6 November 2004.
Barry Smith Jacob Köhler Aanand Kumar	On the Application of Formal Principles to Life Science Data: A Case Study in the Gene Ontology Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration.	E. Rahm (ed.), Database Integration in the Life Sciences (DILS 2004), Berlin: Springer, 2004.
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