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
  •  2006
    Basic concepts of formal ontology
    In Nicola Guarino (ed.), Formal Ontology in Information Systems, Ios Press. pp. 19-28. 1998.
    The term ‘formal ontology’ was first used by the philosopher Edmund Husserl in his Logical Investigations to signify the study of those formal structures and relations – above all relations of part and whole – which are exemplified in the subject-matters of the different material sciences. We follow Husserl in presenting the basic concepts of formal ontology as falling into three groups: the theory of part and whole, the theory of dependence, and the theory of boundary, continuity and contact. T…Read more
  •  404
    Establishing and Harmonizing Ontologies in an Interdisciplinary Health Care and Clinical Research Environment
    with Mathias Brochhausen
    Studies in Health, Technology and Informatics 134 219-234. 2008.
    Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist p…Read more
  •  336
    Some Formal Moments of Truth
    In Werner Leinfellner (ed.), Language and Ontology, Hölder-pichler-tempsky / Reidel. pp. 186-90. 1982.
    A preliminary statement of the formal theory of the truthmaker relation advanced in the paper “Truth-makers” (Mulligan, Simons and Smith) in 1984. Correspondence theories of truth have. I give a brief account of some more or less obvious formal characteristics of this almost forgotten basic truthmaker relation. I then attempt to show how this account may be extended to provide elements of a theory of truth which is in keeping with the spirit of Wittgenstein’s Tractatus.
  •  1281
    Towards an Ontological Representation of Resistance: The Case of MRSA
    with Albert Goldfain and Lindsay G. Cowell
    Journal of Biomedical Informatics 44 (1): 35-41. 2011.
    This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sor…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.
  •  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
  •  986
    Two hundred and sixty-three subjects each gave examples for one of five geographic categories: geographic features, geographic objects, geographic concepts, something geographic, and something that could be portrayed on a map. The frequencies of various responses were significantly different, indicating that the basic ontological terms feature, object, etc., are not interchangeable but carry different meanings when combined with adjectives indicating geographic or mappable. For all of the test p…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”.
  •  462
    SNAP and SPAN: Towards dynamic spatial ontology
    with Pierre Grenon
    Spatial Cognition and Computation 4 (1). 2004.
    We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the inte…Read more
  •  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
  •  2063
    Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object
  •  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
  •  196
    Von T. G. Masaryk bis Jan Patočka: Eine philosophische Skizze
    In J. Zumr & T. Binder (eds.), T. G. Masaryk und die Brentano-Schule, Czech Academy of Sciences. pp. 94-110. 1993.
    Thomas Garrigue Masaryk, later founder and President of the Republic of Czechoslovakia, studied philosophy in the University of Vienna from 1872 to 1876, where he came under the powerful influence of Franz Brentano. We survey the role of Brentano’s philosophy, and especially of his ethics, in Masaryk’s life and work.
  •  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
  •  41
    First published in 1986 and reprinted in 2010 in the Routledge Revivals series, this book presents the first detailed confrontation between the Austrian school of economics and Austrian philosophy, especially the philosophy of the Brentano school. It contains a study of the roots of Austrian economics in the liberal political theory of the nineteenth-century Hapsburg empire, and a study of the relations between the general theory of value underlying Austrian economics and the new economic approa…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
  •  429
    The Role of Foundational Relations in the Alignment of Biomedical Ontologies
    with Cornelius Rosse
    In M. Fieschi, E. Coiera & Y.-C. J. Li (eds.), Medinfo, Ios Press. pp. 444-448. 2004.
    The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characte…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
  •  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).
  •  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
  •  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.
  •  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
  •  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
  •  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