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
  •  223
    More about ontology: Response
    with Louis Goldberg, Michael Glick, and Alan Ruttenberg
    Journal of the American Dental Association 142 (3): 252-254. 2011.
    Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.
  •  189
    Guest Editorial: Ontologies for clinical and translational research
    with Richard H. Scheuermann
    Journal of Biomedical Informatics 44 (1): 3--7. 2011.
  •  283
    The representation of protein complexes in the Protein Ontology
    with Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Judith Blake, and Cathy Wu
    BMC Bioinformatics 12 (371): 1-11. 2011.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consor…Read more
  •  240
    ARGOS policy brief on semantic interoperability
    with Dipak Kalra, Mark Musen, and Werner Ceusters
    Studies in Health Technology and Informatics 170 (1): 1-15. 2011.
    Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained coll…Read more
  •  424
    Wanting what we don't want to want: Representing Addiction in Interoperable Bio-Ontologies
    with Janna Hastings, Nicolas Le Novère, Werner Ceusters, and Kevin Mulligan
    In Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith (eds.), Towards an Ontology of Mental Functioning (ICBO Workshop), Ceur. pp. 56-60. 2012.
    Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most p…Read more
  •  377
    Bioinformatics advances in saliva diagnostics
    with Ji-Ye Ai and David T. W. Wong
    International Journal of Oral Science 4 (2): 85--87. 2012.
    There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the in…Read more
  •  396
    Interdisciplinary perspectives on the development, integration and application of cognitive ontologies
    with Janna Hastings, Gwen Alexandra Frishkoff, Mark Jensen, Russell Poldrack, Jessica Turner, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica A. Turner, and Maryann E. Martone
    Frontiers in Neuroinformatics 8 (62): 1-7. 2014.
    We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for…Read more
  •  464
    Toll-like receptor signaling in vertebrates: Testing the integration of protein, complex, and pathway data in the Protein Ontology framework
    with Cecilia Arighi, Veronica Shamovsky, Anna Maria Masci, Alan Ruttenberg, Darren Natale, Cathy Wu, and Peter D’Eustachio
    PLoS ONE 10 (4). 2015.
    The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse…Read more
  •  527
    The development of non-coding RNA ontology
    with Jingshan Huang, Karen Eilbeck, Judith Blake, Deijing Dou, Weili Huang, Darren Natale, Alan Ruttenberg, Jun Huan, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison Strachan, Nisansa de Silva, and Mohan Vamsi Kasukurthi
    International Journal of Data Mining and Bioinformatics 15 (3): 214--232. 2016.
    Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semant…Read more
  •  469
    Une théorie unifiée de la vérité et de la référence
    In Jean-Maurice Monnoyer (ed.), La Structure Du Monde, Vrin, Paris. pp. 141-184. 2004.
    The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. In what follows we show that the superva…Read more
  •  500
    A Taxonomy of Granular Partitions
    In Thomas Bittner (ed.), Spatial Information Theory. Foundations of Geographic Information Science, Lecture Notes in Computer Science 2205. pp. 28-43. 2001.
    In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed partitions along…Read more
  •  369
    Les objects sociaux
    Philosophique 26 (2). 2002.
    One reason for the renewed interest in Austrian philosophy, and especially in the work of Brentano and his followers, turns on the fact that analytic philosophers have become once again interested in the traditional problems of metaphysics. It was Brentano, Husserl, and the philosophers and psychologists whom they influenced, who drew attention to the thorny problem of intentionality, the problem of giving an account of the relation between acts and objects or, more generally, between the psycho…Read more
  •  721
    How to Do Things with Documents
    Rivista di Estetica 50 179-198. 2012.
    This essay is a contribution to social ontology, drawing on the work of John Searle and of Hernando de Soto. At the center of the argument is the proposition advanced by de Soto in his Mystery of Capital to the effect that many of the entities which structure our contemporary social reality are entities which exist in virtue of the fact that there are (paper or digital) documents which support their existence. I here develop de Soto’s argument further, focusing specifically on the ontological pr…Read more
  •  441
    Putting Biomedical Ontologies to Work
    with Mathias Brochhausen
    Methods of Information in Medicine 49 (2): 135-40. 2010.
    Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT c…Read more
  •  353
    Universal Core Semantic Layer
    with Lowell Vizenor and James Schoening
    In Barry Smith, Lowell Vizenor & James Schoening (eds.), Universal Core Semantic Layer, Ceur, Vol. 555. pp. 1-5. 2009.
    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
  •  553
    Creating a Controlled Vocabulary for the Ethics of Human Research: Towards a biomedical ethics ontology
    with David Koepsell, Robert Arp, and Jennifer Fostel
    Journal of Empirical Research on Human Research Ethics 4 (1): 43-58. 2009.
    Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI)…Read more
  •  975
    Handbook of metaphysics and ontology (edited book)
    with Hans Burkhardt
    Philosophia Verlag. 1991.
    The Handbook of Metaphysics and Ontology reflects the conviction that the history of metaphysics and current work in metaphysics and ontology can each throw valuable light on the other. Thus it is designed to serve both äs a means of making more widely accessible the results of recent scholarship in the history of philosophy, and also äs a unique work of reference in reladon to the metaphysical themes at the centre of much current debate in analyüc philosophy. The work contains more man 450 shor…Read more
  •  1088
    The Information Artifact Ontology (IAO) was created to serve as a domain‐neutral resource for the representation of types of information content entities (ICEs) such as documents, data‐bases, and digital im‐ages. We identify a series of problems with the current version of the IAO and suggest solutions designed to advance our understanding of the relations between ICEs and associated cognitive representations in the minds of human subjects. This requires embedding IAO in a larger framework of on…Read more
  •  30
    Kafka et Brentano
    Philosophiques 26 (2). 1999.
    Un mince fil dans la vaste littérature sur Kafka concerne la connaissance qu’avait Kafka de la philosophie, et plus précisément l’utilisation, dans les récits de Kafka, de quelques-unes des idées principales de Franz Brentano. Kafka a suivi des cours de philosophie à l’Université Charles, cours donnés par des étudiants de Brentano, Anton Marty et Christian von Ehrenfels. Il fut aussi, pendant plusieurs années, membre d’un groupe de discussion organisé par des partisans orthodoxes de la philosoph…Read more
  •  981
    Document Acts
    In Anita Konzelmann Ziv & Hans Bernhard Schmid (eds.), Institutions, Emotions, and Group Agents, Springer. pp. 19-31. 2013.
    The theory of document acts is an extension of the more traditional theory of speech acts advanced by Austin and Searle. It is designed to do justice to the ways in which documents can be used to bring about a variety of effects in virtue of the fact that, where speech is evanescent, documents are continuant entities. This means that documents can be preserved in such a way that they can be inspected and modified at successive points in time and grouped together into enduring document complexes.…Read more
  •  475
    The 2006 Upper Ontology Summit Joint Communiqué
    with Leo Obrst, Patrick Cassidy, Steve Ray, Dagobert Soergel, Matthew West, and Peter Yim
    Applied ontology 1 (2): 203-211. 2006.
    On March 14-15, 2006, at the US National Institute of Standards and Technology (NIST) in Gaithersburg, MD there took place the first Upper Ontology Summit (UOS). This was a convening of custodians of several prominent upper ontologies, key technology participants, and interested other parties, with the purpose of finding a means to relate the different ontologies to each other. The result is reflected in a joint communiqué, directed to the larger ontology community and the general public, and ex…Read more
  •  316
    The formal ontology of boundaries
    Electronic Journal of Analytic Philosophy 5 (5). 1997.
    Revised version published as Barry Smith and Achille Varzi, “Fiat and Bona Fide Boundaries”, Philosophy and Phenomenological Research, 60: 2 (March 2000), 401–420.
  •  373
    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
  •  512
    Brentano and Kafka
    Axiomathes 8 (1): 83-104. 1997.
    There is a narrow thread in the vast literature on Kafka which pertains to Kafka’s knowledge of philosophy, and more precisely to Kafka’s use in his fictional writings of some of the main ideas of Franz Brentano. Kafka attended courses in philosophy at the Charles University given by Brentano’s students Anton Marty and Christian von Ehrenfels, and was for several years a member of a discussion-group organized by orthodox adherents of the Brentanian philosophy in Prague. The present essay summari…Read more
  •  1035
    For much of the first fifty years of its existence, analytic philosophy shunned discussions of normativity and ethics. Ethical statements were considered as pseudo-propositions, or as expressions of pro- or con-attitudes of minor theoretical significance. Nowadays, in contrast, prominent analytic philosophers pay close attention to normative problems. Here we focus our attention on the work of Searle, at the same time drawing out an important connection between Searle’s work and that of two othe…Read more
  •  357
    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
  •  549
    IAO-Intel: An Ontology of Information Artifacts in the Intelligence Domain
    with Tatiana Malyuta, Ron Rudnicki, William Mandrick, David Salmen, Peter Morosoff, Danielle K. Duff, James Schoening, and Kesny Parent
    We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple…Read more
  •  484
    Against idiosyncrasy in ontology development
    In Barry Smith & Christopher Welty (eds.), Formal Ontology in Information Systems (FOIS), Acm Press. pp. 15-26. 2001.
    The world of ontology development is full of mysteries. Recently, ISO Standard 15926 (“Lifecycle Integration of Process Plant Data Including Oil and Gas Production Facilities”), a data model initially designed to support the integration and handover of large engineering artefacts, has been proposed by its principal custodian for general use as an upper level ontology. As we shall discover, ISO 15926 is, when examined in light of this proposal, marked by a series of quite astonishing defects, whi…Read more