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
  •  317
    Applications of the ACGT Master Ontology on Cancer
    with Mathias Brochhausen, Gabriele Weiler, Luis Martín, Cristian Cocos, Holger Stenzhorn, Norbert Graf, Martin Dörr, and Manolis Tsiknakis
    In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the on…Read more
  •  316
    Warum hat sich die deutsche Philosophie so sehr und so langanhaltend an Autoritäten und Texte gebunden gefühlt, fast als ob man – wie die alten Iatrophilologen – Wissen aus bloßen Worten herauspressen wollte? Warum haben sich in Deutschland so häufig philosophische Sprachstile entwickelt, die ein Hindernis fur das Verständnis der entsprechenden Texte sind?
  •  315
    Ontology-driven multicriteria decision support for victim evacuation
    with Linda Elmhadhbi, Mohamed-Hedi Karray, Bernard Archimède, and J. Neil Otte
    International Journal of Information Technology and Decision Making. 2021.
    Abstract In light of the complexity of unfolding disasters, the diversity of rapidly evolving events, the enormous amount of generated information, and the huge pool of casualties, emergency responders (ERs) may be overwhelmed and in consequence poor decisions may be made. In fact, the possibility of transporting the wounded victims to one of several hospitals and the dynamic changes in healthcare resource availability make the decision process more complex. To tackle this problem, we propose a …Read more
  •  315
    基于基本形式化本体的本体构建
    People's Medical Publishing House. 2020.
    In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the…Read more
  •  314
    Developing the Quantitative Histopathology Image Ontology : A case study using the hot spot detection problem
    with Metin Gurcan, Tomaszewski N., Overton John, A. James, Scott Doyle, and Alan Ruttenberg
    Journal of Biomedical Informatics 66 129-135. 2017.
    Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopatholo…Read more
  •  314
    Ontologies for Space and Ground Systems
    In Ground System Architectures Workshop, Gsaw. pp. 1-3. 2020.
    We will survey a range of ontologies relevant to space and ground system domains. The ontologies form part of the Common Core Ontology ecosystem (CCO) developed under the IARPA KDD initiative. We focus specifically on the Space Domain Ontologies, a suite of ontologies to support space situational awareness, including the Spacecraft Mission Ontology, Spacecraft Ontology, Space Event Ontology and Space Object Ontology.
  •  314
    Filozofia austriacka i dziedzictwo Brentany
    Principia 8 19-50. 1994.
    A study of the contrasts between Austrian and German philosophy, with special reference to the role of logic and science, of the Brentano School and the Vienna Circle, and of the different ways in which Austrian and German ways of thinking have influenced contemporary analytical and Continental philosophy.
  •  314
    Ontology: Tool for Broad Spectrum Knowledge Integration (Foreword to Chinese translation of Building Ontologies with Basic Formal Ontology)
  •  313
    On Credentials
    with Olimpia Giuliana Loddo and Giuseppe Lorini
    Journal of Social Ontology 6 (1): 47-67. 2020.
    Credentials play an important role in all modern societies, but the analysis of their nature and function has thus far been neglected by social philosophers. We present a view according to which the function of credentials is certify the identity and the institutional status (including the rights) of individuals. More importantly, credentials enable rights-holders to exercise their rights, so that for a particular right to be exercisable the right-holder should possess, carry and sometimes show …Read more
  •  313
    Truth and the visual field
    In Jean Petitot, Francisco J. Varela, Bernard Pachoud & Jean-Michel Roy (eds.), Naturalizing Phenomenology: Issues in Contemporary Phenomenology and Cognitive Science, Stanford University Press. pp. 317-329. 1999.
    The paper uses the tools of mereotopology (the theory of parts, wholes and boundaries) to work out the implications of certain analogies between the 'ecological psychology' of J. J Gibson and the phenomenology of Edmund Husserl. It presents an ontological theory of spatial boundaries and of spatially extended entities. By reference to examples from the geographical sphere it is shown that both boundaries and extended entities fall into two broad categories: those which exist independently of our…Read more
  •  313
    La verità trionfa: Da T. G. Masaryk a Jan Patočka
    Discipline Filosofiche 2. 1991.
    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.
  •  312
    Vague Reference and Approximating Judgements
    Spatial Cognition and Computation 3 (2). 2003.
    We propose a new account of vagueness and approximation in terms of the theory of granular partitions. We distinguish different kinds of crisp and non-crisp granular partitions and we describe the relations between them, concentrating especially on spatial examples. We describe the practice whereby subjects use regular grid-like reference partitions as a means for tempering the vagueness of their judgments, and we demonstrate how the theory of reference partitions can yield a natural account of …Read more
  •  311
    Relevance, relatedness and restricted set theory
    In Georg Schurz & Georg Jakob Wilhelm Dorn (eds.), Advances in Scientific Philosophy, Rodopi. pp. 45-56. 1991.
    Relevance logic has become ontologically fertile. No longer is the idea of relevance restricted in its application to purely logical relations among propositions, for as Dunn has shown in his (1987), it is possible to extend the idea in such a way that we can distinguish also between relevant and irrelevant predications, as for example between “Reagan is tall” and “Reagan is such that Socrates is wise”. Dunn shows that we can exploit certain special properties of identity within the context of s…Read more
  •  310
    The Industrial Ontologies Foundry (IOF) Core Ontology
    with Milos Drobnjakovic, Boonserm Kulvatunyou, Farhad Ameri, Chris Will, and Albert Jones
    FOMI 2022: 12th International Workshop on Formal Ontologies Meet Industry, September 12-15, 2022, Tarbes, France. 2022.
    The Industrial Ontologies Foundry (IOF) was formed to create a suite of interoperable ontologies. Ontologies that would serve as a foundation for data and information interoperability in all areas of manufacturing. To ensure that each ontology is developed in a structured and mutually coherent manner, the IOF has committed to the tiered architecture of ontology building based on the Basic Formal Ontology (BFO) as top level. One of the critical elements of a successful tiered architecture build i…Read more
  •  310
    Functional anatomy: A taxonomic proposal
    with Ingvar Johansson, Katherine Munn, Nikoloz Tsikolia, Kathleen Elsner, Dominikus Ernst, and Dirk Siebert
    Acta Biotheoretica 53 (3): 153-166. 2005.
    It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.
  •  308
    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
  •  308
    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
  •  307
    Truthmaker realism: Response to Gregory
    Australasian Journal of Philosophy 80 (2): 231-234. 2002.
    We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments are true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of projection, which holds between a judgment p and an objec…Read more
  •  307
    Oncology ontology in the NCI Thesaurus
    with Anand Kumar
    Artificial Intelligence in Medicine 213-220. 2005.
    The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of…Read more
  •  307
    The Plant Ontology: A common reference ontology for plants
    with L. Walls Ramona, D. Cooper Laurel, Elser Justin, W. Stevenson Dennis, Mungall Chris, A. Gandolfo Maria, and Jaiswal Pankaj
    In Walls Ramona L., Cooper Laurel D., Justin Elser, Stevenson Dennis W., Smith Barry, Chris Mungall, Gandolfo Maria A. & Pankaj Jaiswal (eds.), Proceedings of the Workshop on Bio-Ontologies, ISMB, Boston, July, 2010, . 2010.
    The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical stru…Read more
  •  306
    OHMI: The Ontology of Host-Microbiome Interactions
    with Yongqun He, Haihe Wang, Jie Zheng, Daniel P. Beiting, Anna Maria Masci, Hong Yu, Kaiyong Liu, Jianmin Wu, Jeffrey L. Curtis, Alexander V. Alekseyenko, and Jihad S. Obeid
    Journal of Biomedical Semantics 10 (1): 1-14. 2019.
    Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of H…Read more
  •  304
    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
  •  304
    Ontology with Human Subjects Testing: An Empirical Investigation of Geographic Categories
    with David M. Mark
    American Journal of Economics and Sociology 58 (2). 1998.
    Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontologica…Read more
  •  304
    A terminological and ontological analysis of the NCI thesaurus
    with Werner Ceusters and Louis Goldberg
    Methods of Information in Medicine 44 (4): 498-507. 2005.
    We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers…Read more
  •  303
    OntONeo: The Obstetric and Neonatal Ontology
    with Fernanda Farinelli, Mauricio Almeida, and Peter Elkin
    This paper presents the Obstetric and Neonatal Ontology (OntONeo). This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data and to serve interoperability of the associated data and information systems. More generally, it will serve interoperability of clinical and translational data, for example deriving from genomics disciplines and from clinical trials. Interoperability of EHR data is important to ensuring continuity of care during the…Read more
  •  303
    Universal Core Semantic Layer
    with Lowell Vizenor and James Schoening
    The Universal Core (UCore) is a central element of the National Information Sharing Strategy that is supported by multiple U.S. Federal Government Departments, by the intelligence community, and by a number of other national and international institutions. The goal of the UCore initiative is to foster information sharing by means of an XML schema providing consensus representations for four groups of universally understood terms under the headings who, what, when, and where. We here describe a p…Read more
  •  301
    The New European Philosophy
    In János Kristóf Nyíri & Barry Smith (eds.), Philosophy and Political Change in Eastern Europe, Hegeler Institute. pp. 165-170. 1993.
    The paper seeks to indicate ways in which the crude distinction between Anglo-Saxon and Continental philosophy may have to be amended in light of recent developments in Eastern Europe. As is well known, the philosophy of science is to no small part a product of the universities of the Habsburg Empire (in Vienna, Prague, Lemberg/Lwow, etc.). Logic, too, has played a more significant role in Eastern Europe (not least in Poland) than in the philosophical cultures of Germany or France. For these and…Read more
  •  300
    Die ganze Welt ist eine Bühne: Zur Ökologie und Ontologie menschlicher und tierischer Lebenswelt
    Interdisziplinäre Phänomenologie / Interdisciplinary Phenomenology (Kyoto) 1 31-44. 2004.
    Die klassische bikategoriale Ontologie von Substanzen und Akzidentien ist für die Festlegung der Strukturen menschlichen und tierischen Verhaltens nicht hinreichend, da die Umwelten dieses Verhaltens sich nicht in dieses klassische System einfügen. Wir bieten dementsprechend den Grundriß einer Theorie der besonderen Gebilde, die die Alltagswelten menschlicher und tierischer Verhalten konstituieren. Die Ausgangsüberlegung ist die folgende, Wir sind alle (Schau)spieler, und diese brauchen eine Büh…Read more
  •  300
    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
  •  299
    Sechzehn Tage: Wann beginnt ein menschliches Leben?
    In Guido Imaguire & Christine Schneider (eds.), Untersuchungen zur Ontologie, Philosophia. pp. 3-40. 2006.
    Der Abschluß der Gastrulation, der gleichzeitig auch den Anfang der Neurulation bedeutet, ist die zeitliche Grenze, die Beginn eines menschlichen Individuums markiert. Oft wird behauptet, daß jegliche natürliche Veränderung stetig ist. Wie ist es dann aber möglich, eine zeitliche Grenze auszuzeichnen, an der ein menschliches Lebewesen zu existieren beginnt? Man beachte, was geschieht, wenn wir vom Thema zeitlicher Unstetigkeit zum räumlichen übergehen. Lebewesen haben räumliche Grenzen (wie sie …Read more