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
  •  393
    The role of ontologies for sustainable, semantically interoperable and trustworthy EHR solutions
    with Bernd Blobel, Dipak Kalra, Marc Koehn, Ken Lunn, Peter Pharow, Pekka Ruotsalainen, and Stefan Schulz
    Studies in Health Technology and Informatics 150 953-957. 2009.
    As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, seman…Read more
  •  199
    Letter to the Editor: Dealing with socially constructed concepts in an ontology
    Journal of Empirical Research on Human Research Ethics 4 (2): 75-76. 2009.
    Response to the paper “The Biomedical Ethics Ontology Proposal: Excellent Aims, Questionable Methods" by James DuBois, published in the Journal of Empirical Research on Human Research Ethics
  •  478
    Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base
    with Jiye Ai and David Wong
    BMC Bioinformatics 11 (1): 302. 2010.
    The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus…Read more
  •  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
  •  471
    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
  •  739
    Biomedical imaging ontologies: A survey and proposal for future work
    with Sivaram Arabandi, Mathias Brochhausen, Michael Calhoun, Paolo Ciccarese, Scott Doyle, Bernard Gibaud, Ilya Goldberg, Charles E. Kahn Jr, James Overton, John Tomaszewski, and Metin Gurcan
    Journal of Pathology Informatics 6 (37): 37. 2015.
    Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over th…Read more
  •  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
  •  273
    On the ontology of functions
    with Stefano Borgo and Riichiro Mizoguchi
    Applied ontology 6 (2): 99-104. 2011.
    This special issue of Applied Ontology is devoted to the foundation, the comparison and the application of functional theories in all areas, with particular attention to the biological and engineering domains. It includes theoretical and technical contributions related to the description, characterization, and application of functions.
  •  468
    This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to de…Read more
  •  227
    Il significato della vita: come valurare una civiltà
    In Philippe Nemo & Jean Petitot (eds.), Storia del liberalismo in Europa, Rubbettino. 2013.
    In what respects is Western civilization superior or inferior to its rivals? In raising this question we are addressing a particularly strong form of the problem of relativism. For in order to compare civilizations one with another we would need to be in possession of a framework based on principles of evaluation which would be acceptable, in principle, to all human beings. Morality will surely provide one axis of such a framework (and we note in passing that believers in Islam might quite reaso…Read more
  •  278
    A Formal Theory of Substances, Qualities, and Universals
    with Fabian Neuhaus and Pierre Grenon
    One of the tasks of ontology in information science is to support the classification of entities according to their kinds and qualities. We hold that to realize this task as far as entities such as material objects are concerned we need to distinguish four kinds of entities: substance particulars, quality particulars, substance universals, and quality universals. These form, so to speak, an ontological square. We present a formal theory of classification based on this idea, including both a sema…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
  •  378
    The cognitive geometry of war
    In Constraints on Correspondence, Hölder/pichler/tempsky. pp. 394--403. 1989.
    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
  •  543
    The theory of speech acts put forward by Adolf Reinach in his "The A Priori Foundations of the Civil Law" of 1913 rests on a systematic account of the ontological structures associated with various different sorts of language use. One of the most original features of Reinach's account lies in hIs demonstration of how the ontological structure of, say, an action of promising or of commanding, may be modified in different ways, yielding different sorts of non-standard instances of the correspondin…Read more
  •  384
    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
  •  24
    Alexius Meinong, On Objects of Higher Order and Husserl's Phenomenology (review)
    Philosophical Quarterly 30 (120): 252. 1980.
  •  2123
    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