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
  •  510
    The functions of definitions in ontologies
    with Selja Seppälä and Alan Ruttenberg, ,
    To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies.
  •  300
    Relations in Biomedical Ontologies
    with Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kuma, Jane Lomax, Chris Mungall, ,, Fabian Neuhaus, Alan Rector, and Cornelius Rosse
    Genome Biology 6 (5). 2005.
    To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.
  •  613
    The metaphysics of real estate
    Topoi 20 (2): 161-172. 2001.
    The thesis that an analysis of property rights is essential to an adequate analysis of the state is a mainstay of political philosophy. The contours of the type of government a society has are shaped by the system regulating the property rights prevailing in that society. Views of this sort are widespread. They range from Locke to Nozick and encompass pretty much everything else in between. Defenders of this sort of view accord to property rights supreme importance. A state that does not suffici…Read more
  •  395
    Foundations for a Realist Ontology of Mental Disease
    with Werner Ceusters
    Journal of Biomedical Semantics 1 (10): 1-23. 2010.
    While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processe…Read more
  •  886
    Ontologies as Integrative Tools for Plant Science
    with Ramona Walls, Balaji Athreya, Laurel Cooper, Justin Elser, Maria A. Gandolfo, Pankaj Jaiswal, Christopher J. Mungall, Justin Preece, Stefan Rensing, and Dennis W. Stevenson
    American Journal of Botany 99 (8). 2012.
    Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and rela…Read more
  •  452
    Kraus on Weininger, Kraus on Women, Kraus on Serbia
    In Wolfgang Huemer & Marc-Oliver Schuster (eds.), Writing the Austrian Traditions: Relations Between Philosophy and Literature, University of Alberta Press. pp. 81-100. 2003.
    Otto Weininger’s Sex and Character interprets Kant’s categorical imperative in a way which takes it to imply that all human relations, including human sexual relations, are immoral; it is thus in a certain sense impossible to lead a moral life on this earth. We discuss Weininger’s ideas on man, woman, value and intellect, and describe their influence among the Central European intellectuals of his day, including Wittgenstein, and also including Karl Kraus.
  •  316
    LinkSuite™: Software Tools for Formally Robust Ontology-Based Data and Information Integration
    with Werner Ceusters and James Matthew Fielding
    In Werner Ceusters, Barry Smith & James Matthew Fielding (eds.), Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics, 2994), Springer. pp. 1-16. 2004.
    The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an on…Read more
  •  445
    A strategy for improving and integrating biomedical ontologies
    with Cornelius Rosse, Anand Kumar, Jose L. V. Mejino, Daniel L. Cook, and Landon T. Detwiler
    The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate infe…Read more
  •  568
    A survey of theories of part, whole and dependence from Aristotle to the Gestalt psychologists, with special attention to Husserl’s Third Logical Investigation “On the Theory of Parts and Wholes”.
  •  319
    Concept systems and ontologies: Recommendations for basic terminology
    with Gunnar O. Klein
    Transactions of the Japanese Society for Artificial Intelligence 25 (3): 433-441. 2010.
    This is the third draft of a paper that aims to clarify the apparent contradictions in the views presented in certain standards and other specifications of health informatics systems, contradictions which come to light when the latter are evaluated from the perspective of realist philosophy. One of the origins of this document was Klein’s discussion paper of 2005-07-02 entitled “Conceptology vs Reality” and the responses from Smith, as well as the several hours of discussions during the 2005 …Read more
  •  709
    The cornucopia of formal-ontological relations
    with Pierre Grenon
    Dialectica 58 (3). 2004.
    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 threeand four-dimensionalism.
  •  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
  •  1081
    True grid
    In Daniel R. Montello (ed.), Spatial Information Theory: Foundations of Geographic Information Science, Springer. pp. 14-27. 2001.
    The Renaissance architect, moral philosopher, cryptographer, mathematician, Papal adviser, painter, city planner and land surveyor Leon Battista Alberti provided the theoretical foundations of modern perspective geometry. Alberti’s work on perspective exerted a powerful influence on painters of the stature of Albrecht Dürer, Leonardo da Vinci and Piero della Francesca. But his Della pittura of 1435–36 contains also a hitherto unrecognized ontology of pictorial projection. We sketch this ontology…Read more
  •  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
  •  2053
    Function, role and disposition in Basic Formal Ontology
    with Robert Arp
    Proceedings of Bio-Ontologies Workshop, Intelligent Systems for Molecular Biology (ISMB), Toronto. 2008.
    Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivat…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
  •  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
  •  532
    A science of topography: Bridging the qualitative-quantitative divide
    with David M. Mark
    In David M. Mark & Barry Smith (eds.), Geographic Information Science and Mountain Geomorphology, Chichester, England: Springer-praxis. pp. 75--100. 2004.
    The shape of the Earth's surface, its topography, is a fundamental dimension of the environment, shaping or mediating many other environmental flows or functions. But there is a major divergence in the way that topography is conceptualized in different domains. Topographic cartographers, information scientists, geomorphologists and environmental modelers typically conceptualize topographic variability as a continuous field of elevations or as some discrete approximation to such a field. Pilots, …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’.
  •  1096
    Parts and Moments. Studies in Logic and Formal Ontology (edited book)
    Philosophia Verlag. 1982.
    A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar…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
  •  504
    Weininger und Wittgenstein
    Teoria 2. 1984.
    The paper [which is in German] seeks to show how Weininger’s interpretations of Kant and Schopenhauer help us to understand some of the peculiar reflections on the will, on happiness and unhappiness, and on the problems of life, which are to be found in Wittgenstein's Notebooks. It seeks to explain, above all, why Wittgenstein should wish to reject the basic ethical axiom of “love thy neighbor.” There follows a sketch of one possible Kantian interpretation of the Tractatus along Weiningerian lin…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).
  •  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
  •  1090
    The Ontology of Fields (edited book)
    with Donna Peuquet and Berit O. Brogaard
    National Center for Geographic Information and Analysis. 1998.
    In the specific case of geography, the real world consists on the one hand of physical geographic features (bona fide objects) and on the other hand of various fiat objects, for example legal and administrative objects, including parcels of real estate, areas of given soil types, census tracts, and so on. It contains in addition the beliefs and actions of human beings directed towards these objects (for example, the actions of those who work in land registries or in census bureaux), and the rela…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.
  •  476
    Toward a Realistic Science of Environments
    Ecological Psychology 21 (2): 121-130. 2009.
    The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces,…Read more
  •  10
    Ludwig Landgrebe, The Phenomenology of Edmund Husserl. Six Essays (review)
    History and Philosophy of Logic 4 (1): 111. 1983.
  •  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