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
  •  479
    Bridging the gap between medical and bioinformatics: An ontological case study in colon carcinoma
    with Anand Kumar, Yum Lina Yip, and Pierre Grenon
    Computers in Biology and Medicine 36 (7): 694--711. 2006.
    Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in t…Read more
  •  347
    Quality Control for Terms and Definitions in Ontologies and Taxonomies
    with Jacob Köhler, Katherine Munn, Alexander Rüegg, and Andre Skusa
    BMC Bioinformatics 7 (212): 1-12. 2006.
    Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies …Read more
  •  545
    The Neurological Disease Ontology
    with Mark Jensen, Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William Duncan, Patrick Ray, Bianca Weinstock-Guttman, Alan Ruttenberg, Kinga Szigeti, and Alexander D. Diehl
    Journal of Biomedical Semantics 4 (42): 42. 2013.
    We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by…Read more
  •  648
    In Silico Approaches and the Role of Ontologies in Aging Research
    with Georg Fuellen, Melanie Börries, Hauke Busch, Aubrey de Grey, Udo Hahn, Thomas Hiller, Andreas Hoeflich, Ludger Jansen, Georges E. Janssens, Christoph Kaleta, Anne C. Meinema, Sascha Schäuble, Paul N. Schofield, and Others
    Rejuvenation Research 16 (6): 540-546. 2013.
    The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as …Read more
  •  212
    We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The…Read more
  •  445
    Truth­-Makers
    Swiss Philosophical Preprints. 2009.
    During the realist revival in the early years of this century, philosophers of various persuasions were concerned to investigate the ontology of truth. That is, whether or not they viewed truth as a correspondence, they were interested in the extent to which one needed to assume the existence of entities serving some role in accounting for the truth of sentences. Certain of these entities, such as the Sätze an sich of Bolzano, the Gedanken of Frege, or the propositions of Russell and Moore, were…Read more
  •  385
    Vantagens e limitações das ontologias formais na área biomédica
    with Stefan Schulz, Holger Stenzhorn, and Martin Boeker
    RECIIS: Revista Electronica de Comunicacao Informacao, Inovacao Em Saude 3 (1). 2009.
    Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conh…Read more
  •  146
    Die Ontologie des Embryos
    with Berit Brogaard
    In Ludger Jansen & Barry Smith (eds.), Biomedizinische Ontologie: Wissen strukturieren für den Informatik-Einsatz, Utb Forum (vdf). pp. 199-228. 2008.
    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
  •  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
  •  524
    Discussion of “Biomedical informatics: We are what we publish”
    with Geissbuhler Antoine, W. E. Hammond, A. Hasman, R. Hussein, R. Koppel, C. A. Kulikowski, V. Maojo, F. Martin-Sanchez, P. W. Moorman, Moura La, F. G. De Quiros, M. J. Schuemle, Barry Smith, and J. Talmon
    Methods of Information in Medicine 52 (6): 547-562. 2013.
    This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.
  •  408
    ImmPort, toward repurposing of open access immunological assay data for translational and clinical research
    with Sanchita Bhattacharya, Patrick Dunn, Cristel Thomas, Henry Schaefer, Jieming Chen, Zicheng Hu, Kelly Zalocusky, Ravi Shankar, and Shai Shen-Orr
    Scientific Data 5 180015. 2018.
    Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The Im…Read more
  •  405
    Wahrmacher
    with Kevin Mulligan and Peter Simons
    In L. Bruno Puntel (ed.), Der Wahrheitsbegriff: Neue Explikationsversuche, Wissenschaftliche Buchgesellschaft. pp. 210-255. 1987.
    Als zu Beginn des Jahrhunderts der Realismus wieder ernst genommen wurde, gab es viele Philosophen, die sich mit der Ontologie der Wahrheit befaßten. Unabhängig von der Bestimmung der Wahrheit als Korrespondenzbeziehung wollten sie herausfinden, inwieweit zur Erklärung der Wahrheit von Sätzen besondere Entitäten herangezogen werden müssen. Einige dieser Entitäten, so zum Beispiel Bolzanos ‘Sätze an sich’, Freges ‘Gedanken’ oder die ‘propositions’ von Russell und Moore, wurden als Träger der Eige…Read more
  •  1467
    Truth-Makers
    Philosophy and Phenomenological Research 44 (3): 287-321. 1984.
    A realist theory of truth for a class of sentences holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar, we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The core of our theory is the account of truthmaki…Read more
  •  449
    Against Idealism: Johannes Daubert vs. Husserl's Ideas I
    with Karl Schuhmann
    Review of Metaphysics 38 (4): 763-793. 1985.
    In manuscripts of 1930-1 Johannes Daubert, principal member of the Munich board of realist phenomenologists, put forward a series of detailed criticisms of the idealism of Husserl’s Ideas I. The paper provides a sketch of these criticisms and of Daubert’s own alternative conceptions of consciousness and reality, as also of Daubert’s views on perception, similar, in many respects, to those of J. J. Gibson.
  •  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
  •  355
    Nisza
    with Achille C. Varzi
    Filozofia Nauki 3. 2000.
    Pojęcie niszy (otoczenia, kontekstu, siedliska, środowiska) nie cieszy się specjalnym zainteresowaniem ontologów, mimo że ma szerokie zastosowanie w rozmaitych dyscyplinach, od biologii ewolucyjnej po ekonomię. Niniejszy artykuł zawiera pierwszą teorię formalną tego pojęcia — teorię relacji pomiędzy przedmiotami a ich niszami. Teoria ta opiera się na istniejącym dorobku mereologii, topologii i teorii lokalizacji przestrzennej, które są narzędziami ontologii formalnej. Jest ona tutaj ilustrowana …Read more
  •  3822
    Guidelines for writing definitions in ontologies
    with Selja Seppälä and Alan Ruttenberg
    Ciência da Informação 46 (1). 2017.
    Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integr…Read more
  •  332
    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
  •  229
    Ontologische Relationen
    with Ulf Schwarz
    In L. Jansen & Barry Smith (eds.), Biomedizinische Ontologie: Wissen strukturieren für den Informatik-Einsatz, Vdf. pp. 155-172. 2008.
    In Kapitel 5 dieses Buches wurde mit dem ontologischen Sextett eine Klassifizierung der Realität vorgestellt, die das klassische Aristotelische Viereck erweitert, indem sie Einzeldinge und Universalien in insgesamt sechs Kategorien umfaßt. Zwischen den Entitäten dieser Kategorien sind bestimmte Beziehungen postuliert worden, wie zum Beispiel Inhärenz, Partizipation, Instantiierung, Exemplifizierung und Charakterisierung. In diesem Kapitel soil der Frage nachgegangen werden, wie eben diese Bezieh…Read more
  •  439
    Towards new information resources for public health: From WordNet to MedicalWordNet
    with Christane Fellbaum and Udo Hahn
    Journal of Biomedical Informatics 39 (3): 321-332. 2006.
    In the last two decades, WORDNET has evolved as the most comprehensive computational lexicon of general English. In this article, we discuss its potential for supporting the creation of an entirely new kind of information resource for public health, viz. MEDICAL WORDNET. This resource is not to be conceived merely as a lexical extension of the original WORDNET to medical terminology; indeed, there is already a considerable degree of overlap between WORDNET and the vocabulary of medicine. Instead…Read more
  •  1167
    The Emotion Ontology: Enabling Interdisciplinary Research in the Affective Sciences
    with Janna Hastings, Werner Ceusters, and Kevin Mulligan
    In M. Beigl, H. Christiansen, T. Roth-Berghofer, A. Kofod-Petersen, K. R. Coventry & H. R. Schmidtke (eds.), CONTEXT, The Seventh International and Interdisciplinary Conference on Modeling and Using Context, Springer. pp. 119--123. 2011.
    Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of terms 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 disambi…Read more
  •  65
    The Cambridge companion to Husserl (edited book)
    Cambridge University Press. 1995.
    The essays in this volume explore the full range of Husserl's work and reveal just how systematic his philosophy is. There are treatments of his most important contributions to phenomenology, intentionality and the philosophy of mind, epistemology, the philosophy of language, ontology, and mathematics. An underlying theme of the volume is a resistance to the idea, current in much intellectual history, of a radical break between 'modern' and 'postmodern' philosophy, with Husserl as the last of th…Read more
  •  281
    Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in su…Read more
  •  320
    Health Level 7 (HL7) is an international standards development organisation in the domain of healthcare information technology. Initially the mission of HL7 was to enable data exchange via the creation of syntactic standards which supported point-to-point messaging. Currently HL7 sees its mission as one of creating standards for semantic interoperability in healthcare IT on the basis of its flagship “version 3” (v3). Unfortunately, v3 has been plagued by quality and consistency issues, and it ha…Read more
  •  227
    Ontological relations
    with Ulf Schwartz
    In Katherine Munn & Barry Smith (eds.), Applied Ontology, Walter De Gruyter. pp. 219-234. 2008.
  •  1253
    This introduction to the second international conference on Formal Ontology and Information Systems presents a brief history of ontology as a discipline spanning the boundaries of philosophy and information science. We sketch some of the reasons for the growth of ontology in the information science field, and offer a preliminary stocktaking of how the term ‘ontology’ is currently used. We conclude by suggesting some grounds for optimism as concerns the future collaboration between philosophical …Read more
  •  276
    Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associa…Read more
  •  885
    Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our e…Read more
  •  409
    Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that t…Read more
  •  172
    On Forms of Communication In Philosophy
    The Proceedings of the Twentieth World Congress of Philosophy 12 73-82. 2001.
    In previous work, I have drawn attention to certain systematic differences among philosophical traditions as regards to the literary forms that are prevalent in each. In this paper, however, I focus on the commentary form. I raise the question of why the use of commentaries abounds in most traditions except those transmitted in the English language and suggest that problems of translation are central to this issue. I argue that the appearance of commentaries in a philosophical tradition is a cri…Read more