Barry Smith

University at Buffalo
National Center for Ontological Research
  • University at Buffalo
    Department of Philosophy
    Biomedical Informatics
    Neurology
    Computer Science and Engineering
    Distinguished Professor, Julian Park Chair
  • National Center for Ontological Research
    Administrator
  • Università della Svizzera Italiana
    Institute of Philosophy (ISFI)
    Visiting Professor (Part-time)
University of Manchester
Department of Philosophy
PhD, 1976
APA Eastern Division
CV
Buffalo, New York, United States of America
  •  667
    The National Center for Biomedical Ontology
    with Mark A. Musen, Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, and Margaret-Anne Story
    Journal 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
  •  1202
    Towards an ontology of pain
    with Werner Ceusters, Louis J. Goldberg, and Richard Ohrbach
    We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pa…Read more
  •  751
    Ontological realism: A methodology for coordinated evolution of scientific ontologies
    with Werner Ceusters
    Applied 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
  •  464
    This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to de…Read more
  •  18
    See revised version in Barry Smith, Austrian Philosophy, chapter 4; available online at: http://ontology.buffalo.edu/smith/book/austrian_philosophy/
  •  332
    Investigating Subsumption in SNOMED CT: An Exploration into Large Description Logic-Based Biomedical Terminologies
    with Olivier Bodenreider, Anand Kumar, and Anita Burgun
    Artificial 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
  •  195
    Where some have attempted to apply cognitive methods to the study of geography, the present paper is designed to serve as a starting point for applying methods of geographic ontology to the phenomena of cognition. Agglomerations are aggregates of entities that are dispersed through space on geographic scales. Examples include: plagues, biological species, major world religions. The paper applies standard mereotopological theories of spatial regions to agglomerations in this sense. It offers the …Read more
  •  263
    It
    In 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.
  •  373
    The cognitive geometry of war
    In Peter Koller & Klaus Puhl (eds.), Current Issues in Political Philosophy: Justice in Society and World Order, Hölder-pichler-tempsky. pp. 394--403. 1997.
    When national borders in the modern sense first began to be established in early modern Europe, non-contiguous and perforated nations were a commonplace. According to the conception of the shapes of nations that is currently preferred, however, nations must conform to the topological model of circularity; their borders must guarantee contiguity and simple connectedness, and such borders must as far as possible conform to existing topographical features on the ground. The striving to conform to t…Read more
  •  548
    On drawing lines on a map
    In Frank A. U., Kuhn W. & Mark D. M. (eds.), Spatial Information Theory: Proceedings of COSIT '95, Springer. pp. 475-484. 1995.
    The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and trans…Read more
  •  275
    On carcinomas and other pathological entities
    with Anand Kumar, Werner Ceusters, and Cornelius Rosse
    Comparative 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
  •  59
    Surveys the evidence for an influence of Austrian philosophers – specifically Brentano, Meinong, Husserl, Twardowski and Mach – on the early Wittgenstein. Such influence might either have been direct, for instance through Wittgenstein’s reading of Mach, or indirect, through the mediation of Russell and Moore. The paper concludes by addressing the possible influence of Stumpf and Reinach on Wittgenstein’s technical usage of the term ‘Sachverhalt’ in the Tractatus.
  •  428
    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
  •  514
    Traditional vs. Analytic Philosophy (review)
    Grazer Philosophische Studien 21 (1): 193-202. 1984.
    We review an influential series of lectures on analytic philosophy published in 1976 by the West German philosopher Ernst Tugendhat focusing on Tugendhat's treatment of Husserl, and particularly on issues connected with the notion of dependence or Abhängigkeit central to Husserl's philosophy. These issues are of interest not only because Tugendhat's work is one of the few contributions to contemporary analytic philosophy in which they are confronted explicitly, but also because what he has to sa…Read more
  •  328
    Husserlian Ecology
    Human 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
  •  866
    Sixteen days
    Journal of Medicine and Philosophy 28 (1). 2003.
    When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the rel…Read more
  •  3349
    Visceral Values: Aurel Kolnai on Disgust
    In 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
  •  33
    John Searle (edited book)
    Cambridge University Press. 2003.
    From his groundbreaking book Speech Acts to his most recent studies of consciousness, freedom and rationality John Searle has been a dominant and highly influential figure amongst contemporary philosophers. This systematic introduction to the full range of Searle's work begins with the theory of speech acts and proceeds with expositions of Searle's writings on intentionality, consciousness and perception, as well as a careful presentation of the so-called Chinese Room argument. The volume consid…Read more
  •  233
    Les objets sociaux
    Philosophiques 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
  •  2074
    The Relevance of Philosophical Ontology to Information and Computer Science
    In Ruth Hagenbruger & Uwe V. Riss (eds.), Philosophy, computing and information science, Pickering & Chattoo. pp. 75-83. 2014.
    The discipline of ontology has enjoyed a checkered history since 1606, with a significant expansion in recent years. We focus here on those developments in the recent history of philosophy which are most relevant to the understanding of the increased acceptance of ontology, and especially of realist ontology, as a valuable method also outside the discipline of philosophy.
  •  259
    Austria and the rise of scientific philosophy
    In 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
  •  809
    Realistic Phenomenology
    In 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
  •  793
    Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of te rms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disamb…Read more
  •  415
    From concepts to clinical reality: An essay on the benchmarking of biomedical terminologies
    Journal 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
  •  335
    Permanent generic relatedness and silent change
    with Niels Grewe and Ludger Jansen
    In 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
  •  716
    Law and eschatology in Wittgenstein's early thought
    Inquiry: An Interdisciplinary Journal of Philosophy 21 (1-4). 1978.
    The paper investigates the role played by ethical deliberation and ethical judgment in Wittgenstein's early thought in the light of twentieth?century German legal philosophy. In particular the theories of the phenomenologists Adolf Reinach, Wilhelm Schapp, and Gerhart Husserl are singled out, as resting on ontologies which are structurally similar to that of the Tractatus: in each case it is actual and possible Sachverhalte which constitute the prime ontological category. The study of the relati…Read more
  •  535
    The niche
    Noûs 33 (2): 214-238. 1999.
    The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biolo…Read more
  •  732
    Strengths and Limitations of Formal Ontologies in the Biomedical Domain
    Electronic Journal of Communication, Information and Innovation in Health 3 (1): 31-45. 2009.
    We propose a typology of representational artifacts for health care and life sciences domains and associate this typology with different kinds of formal ontology and logic, drawing conclusions as to the strengths and limitations for ontology in a description logics framework. The four types of domain representation we consider are: (i) lexico-semantic representation, (ii) representation of types of entities, (iii) representations of background knowledge, and (iv) representation of individuals. W…Read more
  •  275
    Philosophie und biomedizinische Forschung
    with Bert R. E. Klagges
    Allgemeine Zeitschrift für Philosophie 30 (1). 2005.
    Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifizier…Read more
  •  95
    Brentano’s Ontology: From Conceptualism to Reism
    In Dale Jacquette (ed.), The Cambridge Companion to Brentano, Cambridge University Press. pp. 197-220. 2004.
    It is often claimed that the beginnings of Brentano’s ontology were Aristotelian in nature; but this claim is only partially true. Certainly the young Brentano adopted many elements of Aristotle’s metaphysics, and he was deeply influenced by the Aristotelian way of doing philosophy. But he always interpreted Aristotle’s ideas in his own fashion. He accepted them selectively, and he used them in the service of ends that would not have been welcomed by Aristotle himself. The present paper is an ex…Read more