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447Towards a Reference Terminology for Ontology Research and Development in the Biomedical DomainIn Barry Smith, Waclaw Kusnierczyk, Daniel Schober & Werner Ceusters (eds.), Proceedings of KR-MED, CEUR, vol. 222, . pp. 57-65. 2006.Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have be…Read more
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2542Knowing How vs. Knowing ThatIn J. C. Nyíri & Barry Smith (eds.), Practical Knowledge: Outlines of a Theory of Traditions and Skills, Croom Helm. pp. 1-16. 1988.A sketch of the history of the opposition between propositional and practical knowledge is followed by a brief account of the relevant ideas of Merleau-Ponty, Polanyi, and H. and S. Dreyfus (on expertise and artificial intelligence). The paper concludes with a discussion of the work of Ryle on the notion of a ‘discipline’, drawing implications for a theory of traditions.
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592Ontological tools for geographic representationIn Nicola Guarino (ed.), Formal Ontology in Information Systems (FOIS), Ios Press. pp. 77--85. 1998.This paper is concerned with certain ontological issues in the foundations of geographic representation. It sets out what these basic issues are, describes the tools needed to deal with them, and draws some implications for a general theory of spatial representation. Our approach has ramifications in the domains of mereology, topology, and the theory of location, and the question of the interaction of these three domains within a unified spatial representation theory is addressed. In the final p…Read more
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393Theories of JudgmentIn Thomas Baldwin (ed.), The Cambridge History of Philosophy 1870-1945, Cambridge University Press. pp. 157--173. 2003.The dominant theory of judgment in 1870 was one or other variety of combination theory: the act of judgment is an act of combining concepts or ideas in the mind of the judging subject. In the decades to follow a succession of alternative theories arose to address defects in the combination theory, starting with Bolzano’s theory of propositions in themselves, Brentano’s theory of judgment as affirmation or denial of existence, theories distinguishing judgment act from judgment content advanced by…Read more
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455Why Polish philosophy does not existIn J. Jadacki & J. Pasniczek (eds.), The Lvov-Warsaw School: The New Generation, Reidel. pp. 19-39. 2006.Why have Polish philosophers fared so badly as concerns their admission into the pantheon of Continental Philosophers? Why, for example, should Heidegger and Derrida be included in this pantheon, but not Ingarden or Tarski? Why, to put the question from another side, should there be so close an association in Poland between philosophy and logic, and between philosophy and science? We distinguish a series of answers to this question, which are dealt with under the following headings: (a) the role…Read more
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295Practices of ArtIn J. C. Nyíri & Barry Smith (eds.), Practical Knowledge: Outlines of a Theory of Traditions and Skills, Croom Helm. pp. 172-209. 1988.Starting out from the ontology of human work set out by Marx in Das Kapital, the paper seeks to analyse the relations between the artist and his actions and aims, the work of art he produces, and the audience for this work. The paper concludes with a discussion of the problem of creativity in the arts, drawing on ideas of Roman Ingarden and other phenomenologists.
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18Brentano and Marty: An Inquiry into Being and TruthIn Kevin Mulligan (ed.), Mind, Meaning and Metaphysics: The Philosophy and Theory of Language of Anton Marty, Kluwer Academic Publishers. pp. 111-149. 1990.See revised version in Barry Smith, Austrian Philosophy, chapter 4; available online at: http://ontology.buffalo.edu/smith/book/austrian_philosophy/
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459Beyond PaperThe Monist 97 (2). 2014.The authors outline the way in which documents as social objects have evolved from their earliest forms to the electronic documents of the present day. They note that while certain features have remained consistent, processes regarding document authentication are seriously complicated by the easy reproducibility of digital entities. The authors argue that electronic documents also raise significant questions concerning the theory of ‘documentality’ advanced by Maurizio Ferraris, especially given…Read more
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321Investigating Subsumption in SNOMED CT: An Exploration into Large Description Logic-Based Biomedical TerminologiesArtificial Intelligence in Medicine 39 (3): 183-195. 2007.Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined …Read more
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255ItIn Rudolf Haller & Wolfgang Grassl (eds.), Language, Logic and Philosophy, Reidel. 1980.A brief study of the logical, linguistic, psychological and ontological problem of ‘impersonalia’, which is to say of assertions such as ‘it’s raining’ or ‘es blitzt’ which seem to have no subject. Such assertions cause problems not only for defenders of traditional subject-predicate views of assertive sentences, but also for those, such as Frege, who defended a view in terms of functions and arguments.
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520Logica e ontologia formale nelle «Logische Untersuchungen» di HusserlRivista di Filosofia 83 (1): 53-70. 1991.Per Husserl, come per Bolzano, la logica e una dottrina della sdenza. Husserl prende pero piu sul serio l'idea che le teorie scientifiche siano costituite dagli atti mentali di soggetti conoscenti. Quella che segue e un' esposizione della concezione husserliana della logica e della scienza, fondata appunto sugli atti; essa approdera a una delineazione dell'idea husserliana di «ontologia formale».
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657The National Center for Biomedical OntologyJournal of the American Medical Informatics Association 19 (2): 190-195. 2012.The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variet…Read more
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853The substance of Brentano's ontologyTopoi 6 (1): 39-49. 1987.This paper is a study of Brentano’s ontology, and more specifically of his theory of substance and accident as put forward toward the end of his life in the materials collected together as the Kategorienlehre or Theory of Categories. Here Brentano presents an auditious (re-)interpretation of Aristotle’s theory of substance and accidence. We show that on the Brentano initially defends, it is space which serves as the single substance upon which all other entities depend as accidents of space. In …Read more
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716Ontological realism: A methodology for coordinated evolution of scientific ontologiesApplied ontology 5 (3): 139-188. 2010.Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed fo…Read more
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323Husserlian EcologyHuman Ontology (Kyoto) 7 9-24. 2001.If mind is a creature of adaptation, then our standard theories of intentionality and of mental representation are in need of considerable revision. For such theories, deriving under Cartesian inspiration from the work of Brentano, Husserl and their followers, are context-free. They conceive the subject of mental experience in isolation from any surrounding physico-biological environment. Husserl sought in his later writings to find room for the surrounding world of human practical experience, a…Read more
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482Framework for a protein ontologyBMC Bioinformatics 8 (Suppl 9). 2007.Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relations…Read more
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3310Visceral Values: Aurel Kolnai on DisgustIn Barry Smith & Carolyn Korsmeyer (eds.), Aurel Kolnai's On Disgust, Open Court Publishing Company. pp. 1-23. 2004.In 1929 when Aurel Kolnai published his essay “On Disgust” in Husserl's ]ahrbuch he could truly assert that disgust was a "sorely neglected" topic. Now, however, this situation is changing as philosophers, psychologists, and historians of culture are turning their attention not only to emotions in general but more specifically to the large and disturbing set of aversive emotions, including disgust. We here provide an account of Kolnai’s contribution to the study of the phenomenon of disgust, of …Read more
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679The Neurath-Haller Thesis: Austria and the Rise of Scientific PhilosophyIn Keith Lehrer & Johann Christian Marek (eds.), Austrian Philosophy Past and Present, Kluwer Academic Publishers. pp. 1-20. 1997.The term ‘Continental philosophy’ designates not philosophy on the continent of Europe as a whole, but rather a selective slice of Franco-German philosophy. Through a critical analysis of the arguments advanced by Otto Neurath, the paper addresses the issue of why Austrian philosophers in particular are not counted in the pantheon of Continental philosophers. Austrian philosophy is marked by the predominance of philosophical analysis and of the philosophy of science. The paper concludes that it …Read more
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259On carcinomas and other pathological entitiesComparative and Functional Genomics 6 (7/8). 2005.Tumors, abscesses, cysts, scars, fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transform…Read more
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357A realism-based approach to the evolution of biomedical ontologiesIn Proceedings of the Annual AMIA Symposium, American Medical Informatics Association. pp. 121-125. 2006.We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles …Read more
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1592The Space Object OntologyIn Alexander P. Cox, Christopher Nebelecky, Ronald Rudnicki, William Tagliaferri, John L. Crassidis & Barry Smith (eds.), 19th International Conference on Information Fusion (FUSION 2016), Ieee. 2016.Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missio…Read more
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800Realistic PhenomenologyIn Lester Embree (ed.), Encyclopedia of Phenomenology, Springer Science & Business Media. pp. 586-590. 1997.The tradition of realist phenomenology was founded in around 1902 by a group of students in Munich interested in the newly published Logical Investigations of Edmund Husserl. Initial members of the group included Johannes Daubert, Alexander Pfänder, Adolf Reinach and Max Scheler. With Reinach’s move to Göttingen the group acquired two new prominent members – Edith Stein and Roman Ingarden. The group’s method turned on Husserl’s idea that we are in possession a priori (which is to say: non-induct…Read more
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405From concepts to clinical reality: An essay on the benchmarking of biomedical terminologiesJournal of Biomedical Informatics 39 (3): 288-298. 2006.It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys som…Read more
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272Philosophy and Biomedical Information SystemsIn Katherine Munn & Barry Smith (eds.), Applied Ontology: An Introduction, Ontos. pp. 17-30. 2008.The pathbreaking scientific advances of recent years call for a new philosophical consideration of the fundamental categories of biology and its neighboring disciplines. Above all, the new information technologies used in biomedical research, and the necessity to master the continuously growing flood of data that is associated therewith, demand a profound and systematic reflection on the systematization and classification of biological data. This, however, demands robust theories of basic concep…Read more
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309Permanent generic relatedness and silent changeIn Niels Grewe, Ludger Jansen & Barry Smith (eds.), Formal Ontology and Information Systems, Ceur, Vol. 1060. pp. 1-5. 2016.Given the assertion of a relation between two types, like: “Epidermis has part some Keratinocyte”, we define silent change as any kind of change of the instance-relata of the relation in question that does not change the truth-value of the respective type-level assertion. Such assertions are notoriously difficult to model in OWL 2. To address this problem, we distinguish different modes of type-level relatedness giving rise to this problem and describe a conservative extension to the BFO top-le…Read more
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431Truthmaker ExplanationsIn Jean-Maurice Monnoyer (ed.), Metaphysics and Truthmakers, Ontos Verlag. pp. 79-98. 2007.This paper is a fresh attempt to articulate the role of a theory of truthmakers. We argue that truthmaker theory constitutes a cornerstone of good methodology in metaphysics, but that a conflation of truthmaker theory with the theory of truth has been responsible for certain excesses associated with truthmaker-based approaches in the recent literature. If truthmaker theory is not a component of a theory of truth, then truthmaker maximalism – the view that every truth has a truthmaker – loses its…Read more
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225Les objets sociauxPhilosophiques 26 (2): 315-347. 1999.One reason for the renewed interest in Austrian philosophy, and especially in the work of Brentano and his followers, turns on the fact that analytic philosophers have become once again interested in the traditional problems of metaphysics. It was Brentano, Husserl, and the philosophers and psychologists whom they influenced, who drew attention to the thorny problem of intentionality, the problem of giving an account of the relation between acts and objects or, more generally, between the psycho…Read more
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1937The Substitution Theory of ArtGrazer Philosophische Studien 25 (1): 533-557. 1985.In perceptual experience we are directed towards objects in a way which establishes a real relation between a mental act and its target. In reading works of fiction we enjoy experiences which manifest certain internal similarities to such relational acts, but which lack objects. The substitution theory of art attempts to provide a reason why we seek out such experiences and the artifacts which they generate. Briefly, we seek out works of art because we enjoy the physiology and the phenomenology …Read more
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254Austria and the rise of scientific philosophyIn Arkadiusz Chrudzimski & Wolfgang Huemer (eds.), Phenomenology and analysis: essays on Central European philosophy, Ontos. pp. 33-56. 2004.The term ‘Continental philosophy’ designates not philosophy on the continent of Europe as a whole, but rather a selective slice of Franco-German philosophy. Through a critical analysis of the arguments advanced by Otto Neurath, the paper addresses the issue of why Austrian philosophers in particular are not counted in the pantheon of Continental philosophers. Austrian philosophy is marked by the predominance of philosophical analysis and of the philosophy of science. The paper concludes that it …Read more
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908Individuals, universals, collections: On the foundational relations of ontologyIn Achille Varzi Laure Vieu (ed.), ”, Formal Ontology in Information Systems. Proceedings of the Third International Conference, Ios Press. 2004.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 …Read more
Barry Smith
University at Buffalo
National Center for Ontological Research
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University at BuffaloDepartment of Philosophy
Biomedical Informatics
Neurology
Computer Science and EngineeringDistinguished Professor, Julian Park Chair -
National Center for Ontological ResearchAdministrator
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APA Eastern Division
Buffalo, New York, United States of America
Areas of Specialization
Metaphysics |
Ontology |
Philosophy of Artificial Intelligence |
Philosophy of Biology |