• University at Buffalo
    Department of Philosophy
    Biomedical Informatics
    Neurology
    Computer Science and Engineering
    Distinguished Professor, Julian Park Chair
University of Manchester
Department of Philosophy
PhD, 1976
APA Eastern Division
CV
Buffalo, New York, United States of America
  • Biomedical Ontologies
    In Peter Elkin (ed.), Terminology, Ontology and their Implementations, Springer Nature Switzerland Ag. forthcoming.
    We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of the term…Read more
  • Making AI Meaningful Again
    Synthese 198 (March): 2061-2081. 2021.
    Artificial intelligence (AI) research enjoyed an initial period of enthusiasm in the 1970s and 80s. But this enthusiasm was tempered by a long interlude of frustration when genuinely useful AI applications failed to be forthcoming. Today, we are experiencing once again a period of enthusiasm, fired above all by the successes of the technology of deep neural networks or deep machine learning. In this paper we draw attention to what we take to be serious problems underlying current views of artifi…Read more
  • CIDO: The Community-Based Coronavirus Infectious Disease Ontology
    Yongqun He, Y. J. Hong, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-hui Huang, John Beverley, Asiyah Yu Lin, Duncan William D., Sivaram Arabandi, Jiangan Xie, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, Brian Athey, and Barry Smith
    Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) and 10th Workshop on Ontologies and Data in Life Sciences (ODLS). 2021.
    Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have init…Read more
  • Truthmaker realism
    Australasian Journal of Philosophy 77 (3). 1999.
    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
  • Amongst the entities making up social reality, are there necessary relations whose necessity is not a mere reflection of the logical connections between corresponding concepts? We distinguish three main groups of answers to this question, associated with Hume and Adolf Reinach at opposite extremes, and with Searle who occupies a position somewhere in the middle. We first set forth Reinach’s views on what he calls ‘material necessities’ in the realm of social entities. We then attempt to show tha…Read more
  • The Ontology of Fields (edited book)
    Donna Peuquet, Barry Smith, and Berit Brogaard
    National Center for Geographic Information and Analysis. 1998.
    In the specific case of geography, the real world consists on the one hand of physical geographic features (bona fide objects) and on the other hand of various fiat objects, for example legal and administrative objects, including parcels of real estate, areas of given soil types, census tracts, and so on. It contains in addition the beliefs and actions of human beings directed towards these objects (for example, the actions of those who work in land registries or in census bureaux), and the rela…Read more
  • Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology
    John Beverley, Shane Babcock, Gustavo Carvalho, Lindsay Cowell, Sebastian Duesing, Regina Hurley, and Barry Smith
    Open Science Foundation Preprints. 2020.
    Rapidly, accurately and easily interpreting generated data is of fundamental concern. Ontologies – structured controlled vocabularies – support interoperability and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontologies (OBO) Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological conte…Read more
  • CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis
    Oliver He, John Beverley, Gilbert S. Omenn, Barry Smith, Brian Athey, Luonan Chen, Xiaolin Yang, Junguk Hur, Hsin-hui Huang, Anthony Huffman, Yingtong Liu, Yang Wang, Edison Ong, and Hong Yu
    Scientific Data 181 (7): 5. 2020.
    Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), w…Read more
  • Ontology and Cognitive Outcomes
    David Limbaugh, Jobst Landgrebe, David Kasmier, Ronald Rudnicki, James Llinas, and Barry Smith
    Journal of Knowledge Structures and Systems 1 (1). 2020.
    The term ‘intelligence’ as used in this paper refers to items of knowledge collected for the sake of assessing and maintaining national security. The intelligence community (IC) of the United States (US) is a community of organizations that collaborate in collecting and processing intelligence for the US. The IC relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a…Read more
  • The Infectious Disease Ontology in the Age of COVID-19
    Shane Babcock, Lindsay G. Cowell, John Beverley, and Barry Smith
    Journal of Biomedical Semantics 12 (13). 2021.
    The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and patho…Read more
  • What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arr…Read more
  • In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will imp…Read more
  • Ontology
    In Luciano Floridi (ed.), Blackwell Guide to the Philosophy of Computing and Information, Blackwell. pp. 155-166. 2003.
    Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by philosophers, the ter…Read more
  • Quantum mereotopology
    Barry Smith and Berit O. Brogaard
    Annals of Mathematics and Artificial Intelligence 36 (1): 153-175. 2002.
    Mereotopology faces problems when its methods are extended to deal with time and change. We offer a new solution to these problems, based on a theory of partitions of reality which allows us to simulate (and also to generalize) aspects of set theory within a mereotopological framework. This theory is extended to a theory of coarse- and fine-grained histories (or finite sequences of partitions evolving over time), drawing on machinery developed within the framework of the so-called ‘consistent hist…Read more
  • Foundations for a Realist Ontology of Mental Disease
    Werner Ceusters and Barry Smith
    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