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
  •  618
    In defense of extreme (fallibilistic) apriorism
    Journal of Libertarian Studies 12 (1). 1996.
    We presuppose a position of scientific realism to the effect (i) that the world exists and (ii) that through the working out of ever more sophisticated theories our scientific picture of reality will approximate ever more closely to the world as it really is. Against this background consider, now, the following question: 1. Do the empirical theories with the help of which we seek to approximate a good or true picture of reality rest on any non-empirical presuppositions? One can answer this quest…Read more
  •  658
    The Protein Ontology: A structured representation of protein forms and complexes
    with Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Jian Zhang, and Cathy H. Wu
    Nucleic Acids Research 39 (1). 2011.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate repres…Read more
  •  10
    Ludwig Landgrebe, The Phenomenology of Edmund Husserl. Six Essays (review)
    History and Philosophy of Logic 4 (1): 111. 1983.
  •  526
    The structures of the common-sense world
    Acta Philosophica Fennica 58. 1995.
    While contemporary philosophers have devoted vast amounts of attention to the language we use in describing and finding our way about the world of everyday experience, they have, with few exceptions, refused to see this world itself as a fitting object of theoretical concern. In what follows I shall seek to show how the commonsensical world might be treated ontologically as an object of investigation in its own right. At the same time I shall seek to establish how such a treatment might help us …Read more
  •  364
    On the Austrianness of Austrian economics
    Critical Review: A Journal of Politics and Society 4 (1-2): 212-238. 1990.
    Much recent work on the intellectual background of Austrian economics reveals an unfortunate lack of awareness of the distinct nature of the Austrian contribution to philosophy, from which the Austrian economists drew many of their ideas. The present essay offers a sketch of this contribution, contrasting Austrian philosophy especially with the modes of philosophy dominant in Germany. This makes it possible to throw new light on the relations on Mises, Kant and the Vienna circle, and it allows u…Read more
  •  351
    Constraints on Correspondence
    In H. Rutte, W. Sauer & W. Gombocz (eds.), Traditionen und Perspektiven der analytischen Philosophie: Festschrift für Rudolf Haller, Hölder/pichler/tempsky. pp. 415-430. 1989.
    My aim is to lay down some constraints on a correspondence theory of truth for empirical sentences of a natural language on the basis of a theory according to which that to which a true empirical sentence of such a language corresponds is a part of the natural world. The problem is to find some means of delineating those portions of the world which serve as correspondents, portions of reality otherwise called ‘truthmakers’.
  •  322
    Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this rea…Read more
  •  644
    Basic Formal Ontology for bioinformatics
    with Anand Kumar and Thomas Bittner
    IFOMIS Reports. 2005.
    Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith…Read more
  •  298
    Horizontal Integration of Warfighter Intelligence Data: A Shared Semantic Resource for the Intelligence Community
    with Tatiana Malyuta, William S. Mandrick, Chia Fu, Kesny Parent, and Milan Patel
    In Barry Smith, Tatiana Malyuta, William S. Mandrick, Chia Fu, Kesny Parent & Milan Patel (eds.), Proceedings of the Conference on Semantic Technology in Intelligence, Defense and Security (STIDS), CEUR, . pp. 1-8. 2012.
    We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping …Read more
  •  278
    Biomedical informatics and granularity
    with Anand Kumar
    Comparative and Functional Genomics 5 (6-7): 501-508. 2004.
    An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).
  •  1268
    Formal ontology, common sense, and cognitive science
    International Journal of Human-Computer Studies 43 (5-6). 1995.
    Common sense is on the one hand a certain set of processes of natural cognition - of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific treatment of this world relate to…Read more
  •  443
    What follows is an investigation of the ontology of Franz Brentano with special reference to Brentano's later and superficially somewhat peculiar doctrine to the effect that the substances of the material world are three dimensional places. Taken as a whole, Brentano's philosophy is marked by three, not obviously compatible, trait. In the first place, his work is rooted in the metaphysics of Aristotle, above all in Aristotle's substance/accident ontology and in the Aristotelian …Read more
  •  371
    Building on the writings of Wittgenstein on rule-following and deviance, Kristóf Nyíri advanced a theory of creativity as consisting in a fusion of conflicting rules or disciplines. Only such fusion can produce something that is both intrinsically new and yet capable of being apprehended by and passed on to a wider community. Creativity, on this view, involves not the breaking of rules, or the deliberate cultivation of deviant social habits, but rather the acceptance of enriched systems of rules…Read more
  •  308
    The piece of wax takes on the form of the seal; but this occurs in a way that is largely indifferent to the particular constitution of the seal. Similarly, Aristotle says, ‘the sense is affected by what is coloured or flavoured or sounding, but it is indifferent as to what in each case the substance is’. We show that Brentano takes this Aristotelian account of the relation between sense and its objects as the basis for his theory of mind in the Psychology from an Empirical Standpoint.
  •  411
    Standard theories in mereotopology focus on relations of parthood and connection among spatial or spatio-temporal regions. Objects or processes which might be located in such regions are not normally directly treated in such theories. At best, they are simulated via appeal to distributions of attributes across the regions occupied or by functions from times to regions. The present paper offers a richer framework, in which it is possible to represent directly the relations between entities of var…Read more
  •  614
    CARO: The Common Anatomy Reference Ontology
    with Melissa Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, José L. V. Mejino Jr, and Chris J. Mungall
    The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and…Read more
  •  3381
    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 influe…Read more
  •  224
    Imagine a 5-stone weakling whose brain has been loaded with all the knowledge of a champion tennis player. He goes to serve in his first match – Wham! – His arm falls off. The 5-stone weakling just doesn’t have the bone structure or muscular development to serve that hard. There are, clearly, different types of knowledge/ability/skill, only some of which are a matter of what can be transferred simply by passing signals down a wire from one brain (or computer) to another. Sometimes it is the body…Read more
  •  558
    Metaphysics
    In Asbjørn Steglich-Petersen (ed.), Metaphysics: Five Questions, Automatic Press. pp. 143-158. 2010.
    Attempts to trace a unifying thread of ontological realism extending through 1. my early writings on Frege, Brentano, Husserl, Wittgenstein, Ingarden and (with Kevin Mulligan and Peter Simons) on truthmakers; 2. work on formal theories of the common-sense world, and on mereotopology, fiat objects, geographical categories, and environments (with David Mark, Roberto Casati, Achille Varzi), to 3. current work on applied ontology in biology and medicine, and on the theory of document acts and on the…Read more
  •  632
    An Essay on Material Necessity
    Canadian Journal of Philosophy (sup1): 301-322. 1992.
    Where Humeans rule out the possibility of material or non-logical necessity, and thus of any associated knowledge a priori, the German legal philosopher Adolf Reinach defends the existence of a wide class of material necessities falling within the domain of what can be known a priori, for example in fields such as color and shape, rational psychology, law and economics. Categories such as promise or claim or obligation are, in Reinach’s view, exist as nodes in a system of necessary relations, so…Read more
  •  488
    The Unified Medical Language System and the Gene Ontology: Some critical reflections
    with Anand Kumar
    In A. Günter, R. Kruse & B. Neumann (eds.), KI 2003: Advances in Artificial Intelligence, Springer. pp. 135-148. 2003.
    The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to a…Read more
  •  552
    Granular Partitions and Vagueness
    In Chris Welty & Barry Smith (eds.), Formal Ontology in Information Systems (FOIS), Acm Press. pp. 309-320. 2003.
    There are some who defend a view of vagueness according to which there are intrinsically vague objects or attributes in reality. Here, in contrast, we defend a view of vagueness as a semantic property of names and predicates. All entities are crisp, on this view, but there are, for each vague name, multiple portions of reality that are equally good candidates for being its referent, and, for each vague predicate, multiple classes of objects that are equally good candidates for being its extensio…Read more
  •  1326
    Framework for formal ontology
    Topoi 2 (1): 73-85. 1983.
    The discussions which follow rest on a distinction, first expounded by Husserl, between formal logic and formal ontology. The former concerns itself with (formal) meaning-structures; the latter with formal structures amongst objects and their parts. The paper attempts to show how, when formal ontological considerations are brought into play, contemporary extensionalist theories of part and whole, and above all the mereology of Leniewski, can be generalised to embrace not only relations between c…Read more
  •  273
    Tracking Referents in Electronic Health Records
    with Werner Ceusters
    Studies in Health Technology and Informatics 116. 2005.
    Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in which a…Read more
  •  199
    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
  •  378
    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
  •  691
    Logic and the Sachverhalt
    The Monist 72 (1): 52-69. 1989.
    Those who conceive logic as a science have generally favoured one of two alternative conceptions as to what the subject-matter of this science ought to be. On the one hand is the nowadays somewhat old-fashioned-seeming view of logic as the science of judgment, or of thinking or reasoning activities in general. On the other hand is the view of logic as a science of ideal meanings, 'thoughts', or 'propositions in themselves'. There is, however, a third alternative conception, which enjoyed only a …Read more
  •  368
    Toward an Ontological Treatment of Disease and Diagnosis
    with Richard H. Scheuermann and Werner Ceusters
    In Proceedings of the 2009 AMIA Summit on Translational Bioinformatics, American Medical Informatics Association. 2009.
    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 disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological process…Read more
  •  1209
    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
  •  466
    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