• University at Buffalo
    Department of Philosophy
    Biomedical Informatics
    Computer Science and Engineering
    Distinguished Professor, Julian Park Chair
University of Manchester
Department of Philosophy
PhD, 1976
APA Eastern Division
Buffalo, New York, United States of America
  •  23
    Common Core Conformant Definitions for an Ontology of Commercial Exchange
    2nd International Workshop on Ontology of Social, Legal and Economic Entities (SoLEE). 2021.
    In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domai…Read more
  •  56
    Benefits of Realist Ontologies to Systems Engineering
    with Eric Merrell, Robert M. Kelly, David Kasmier, Marc Brittain, Ronald Ankner, Evan Maki, Curtis W. Heisey, and Kevin Bush
    8th International Workshop on Ontologies and Conceptual Modelling (OntoCom). 2021.
    Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) int…Read more
  • Christian von Ehrenfels was a student of both Franz Brentano and Carl Menger and his thinking on value theory was inspired both by Brentano’s descriptive psychology and by the subjective theory of economic value advanced by Menger, the founder of the Austrian school of economics. Value, for Ehrenfels, is a function of desire, and we ascribe value to those things which we either do in fact desire, or would desire if we were not convinced of their existence. He asserts that the needed theoretical …Read more
  •  16
    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
  • 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. forthcoming.
    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
  •  14
    Adolf Reinach: An annotated bibliography
    In Speech Act and Sachverhalt. Reinach and the Foundations of Realist Phenomenology, . pp. 299-332. 1987.
    Reinach is principally known for his anticipation in 1913 of many ideas subsequently developed by Austin, Searle and others under the heading of 'speech act theory'. This bibliography of primary and secondary literature by and on Reinach shows that his influenced extended more broadly into areas such as the theory of judgment, the ontology of states of affairs, and the philosophy of law.
  •  14
    The Industrial Ontologies Foundry (IOF) perspectives
    with Mohamed Karray, Neil Otte, Rahul Rai, Farhad Ameri, Boonserm Kulvatunyou, Dimitris Kiritsis, Chris Will, Rebecca Arista, and Others
    Proceedings: Industrial Ontology Foundry (IOF) Achieving Data Interoperability Workshop, International Conference on Interoperability for Enterprise Systems and Applications, Tarbes, France, March 17-24, 2020. 2021.
    In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous …Read more
  •  25
    OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies
    with Rebecca C. Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D. Diehl, Damion Dooley, William Duncan, Nomi L. Harris, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Christian J. Stoeckert, Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, and Bjoern Peters
    Bioarchiv. 2021.
    Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of ov…Read more
  •  79
    Making Space: The Natural, Cultural, Cognitive and Social Niches of Human Activity
    Cognitive Processing 22 (supplementary issue 1): 77-87. 2021.
    This paper is in two parts. Part 1 examines the phenomenon of making space as a process involving one or other kind of legal decision-making, for example when a state authority authorizes the creation of a new highway along a certain route or the creation of a new park in a certain location. In cases such as this a new abstract spatial entity comes into existence – the route, the area set aside for the park – followed only later by concordant changes in physical reality. In Part 2 we show that f…Read more
  •  23
    On the Theory of the Negative Judgment
    with Adolf Reinach
    In Barry Smith (ed.), Parts and Moments. Studies in Logic and Formal Ontology, Philosophia Verlag. 1882.
    Distinguishes two senses of 'judgment' on the one hand as meaning a state of 'conviction' or 'belief', and on the other hand as meaning an act of 'affirmation' or 'assertion'. Certainly conviction and assertion stand in close relation to each other, but they delineate two heterogeneous logical spheres, and thereby divide the total field of the theory of judgment into two neighbouring but separate sub-fields. Once this is done it is shown to have implications for our understanding especially of …Read more
  •  13
    Gestalt level and Gestalt purity (trans. B. Smith)
    with Christian von Ehrenfels
    In Barry Smith (ed.), Foundations of Gestalt Theory, Philosophia. pp. 118-120. 1988.
    The fact that there is such a thing as a degree of formedness [Gestaltung], that every Gestalt has a certain Gestalt level, is of fundamental significance. A rose is a Gestalt of higher level than a heap of sand: this we recognize just as immediately as that red is a fuller, more lively colour than grey. The higher Gestalten are distinguished further from the lower by the fact that the product of unity and multiplicity [Einheit und Mannigfaltigkeit] is in their case greater.
  •  28
    On 'Gestalt qualities' (trans. B. Smith)
    with C. Von Ehrenfels
    In Barry Smith (ed.), Foundations of Gestalt Theory, Philosophia. pp. 82--117. 1988.
    The theory of Gestalt qualities arose from the attempt to explain how a melody is distinct from the collection of the tones which it comprehends. In this essay from 1890 Christian von Ehrenfels coined the term 'Gestaltqualität' to capture the idea of a pattern which is comprehensible in a single experience. This idea can be applied not only to melodies and other occurrent patterns, but also to continuant patterns such as shapes and colour arrays such as the array of a chess board. Ehrenfel's ess…Read more
  •  21
    Neural Chitchat
    The Sherry Turkle Miracle. 2021.
    A constant theme in Sherry Turkle’s work is the idea that computers shape our social and psychological lives. This idea is of course in a sense trivial, as can be observed when walking down any city street and noting how many of the passers-by have their heads buried in screens. In The Second Self, however, Turkle makes a stronger claim to the effect that where people confront machines that seem to think this suggests a new way for us to think – about human thought, emotion, memory, and understa…Read more
  •  32
    Ontology (Science)
    In Carola Eschenbach & Mike Grüninger (eds.), Formal Ontology in Information Systems. Proceedings of the Fifth International Conference (FOIS 2008), Amsterdam: Ios Press. pp. 21-35. 2008.
    Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some…Read more
  •  60
    Living High and Letting Die
    with Nicola Bourbaki and Berit Brogaard
    Philosophy 76 (297). 2001.
    Imagine that your body has become attached, without your permission, to that of a sick violinist. The violinist is a human being. He will die if you detach him. Such detachment seems, nonetheless, to be morally permissible. Thomson argues that an unwantedly pregnant woman is in an analogous situation. Her argument is considered by many to have established the moral permissibility of abortion even under the assumption that the foetus is a human being. Another popular argument is that presented by…Read more
  •  30
    Wind Turbine Analysis Project
    with Neil Otte, Rahul Rai, and Clare Paul
    Final Project Report. 2018.
    The report describes an application of ontologies to the analysis of wind turbine manufacturing data. We show how applying ontologies to composite materials data may facilitate the discovery of optimum composite material designs that will deliver maximum wind turbine blade performance within environmental constraints.
  •  51
    CIDO: The Community-Based Coronavirus Infectious Disease Ontology
    with Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-hui Huang, Beverley John, Asiyah Yu Lin, Duncan William D., Sivaram Arabandi, Jiangan Xie, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, and Brian Athey
    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
  •  41
    CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIViewH
    with Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Martin Hofmann-Apitius, Yongqun Oliver He, and Alpha Tom Kodamullil
    Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) and 10th Workshop on Ontologies and Data in Life Sciences (ODLS). 2021.
    Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is lin…Read more
  •  148
    Publications by Barry Smith
    Cosmos + Taxis 4 (4): 67-104. 2017.
  •  55
    In the present review we focus on what we take to be some remaining issues with the Behaviour Change Intervention Ontology (BCIO). We are in full agreement with the authors’ endorsement of the principles of best practice for ontology development In particular, we agree that an ontology should be “logically consistent and having a clear structures [sic], preferably a well-organised hierarchical structure,” and that “Maximising the new ontology’s interoperability with existing ontologies by reusin…Read more
  •  173
    Conceptual Spaces for Space Event Characterization via Hard and Soft Data Fusion
    with Jeremy R. Chapman, David Kasmier, David Limbaugh, Stephen R. Gagnon, John Crassidis, James Llinas, and Alexander P. Cox
    AIAA (American Institute of Aeronautics and Astronautics) Scitech 2021 Forum. 2021.
    The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This pr…Read more
  •  31
    Gustav Bergmann, New Foundations of Ontology (review)
    Vienna Circle Institute Yearbook 3 304-306. 1995.
    The formal ontology here presented is what we might call a typed combinatorial Meinongian mereology. Its author seeks to formulate the laws, here called ‘canons’, regulating how entities can combine together in wholes of different sorts. The method, as in Bergmann’s earlier works, involves the construction of an ideal language of such a sort that the analysis of complex wholes can be achieved by transforming our natural-language representations of reality into what we might think of as artificia…Read more
  •  83
    Ontology: Tool for Broad Spectrum Knowledge Integration (Foreword to Chinese translation of Building Ontologies with Basic Formal Ontology)
  •  82
    with Robert Arp and Andrew D. Spear
    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
  •  50
    Le credenziali: parole, disegni e poteri deontici
    Teoria E Critica Della Regolazione Sociale 1 (20). 2020.
    Driving licenses, identity cards, passports, boarding passes, credit cards, ATM cards – all of these are examples of credentials. Credentials are documents that play a fundamental role in all modern societies. However, philosophers and social ontologists have not yet addressed the analysis of their nature and function. This paper aims to fill this gap through a review of the essential characteristics of credentials, as documents whose primary purpose is to certify the identity and institutional …Read more
  •  106
    PROMES: An ontology‐based messaging service for semantically interoperable information exchange during disaster response
    with Linda Elmhadhbi, Mohamed‐Hedi Karray, Bernard Archimède, and J. Neil Otte
    Journal of Contingencies and Crisis Management 28 (3): 324-338. 2020.
    Disaster response requires the cooperation of multiple emergency responder organizations (EROs). However, after‐action reports relating to large‐scale disasters identity communication difficulties among EROs as a major hindrance to collaboration. On the one hand, the use of two‐radio communication, based on multiple orthogonal frequencies and uneven coverage, has been shown to degrade inter‐organization communication. On the other hand, because they reflect different areas of expertise, EROs use…Read more
  •  409
    Conceptual Space Modeling for Space Event Characterization
    with Jeremy R. Chapman, David Kasmier, David Limbaugh, Stephen R. Gagnon, John L. Crassidis, James Llinas, and Alexander Cox
    IEEE 23rd International Conference on Information Fusion (FUSION). 2020.
    This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. …Read more
  •  287
    Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology
    with John Beverley, Shane Babcock, Gustavo Carvalho, Lindsay Cowell, Sebastian Duesing, and Regina Hurley
    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
  •  2
    A Semantics-Based Common Operational Command System for Multiagency Disaster Response
    with Linda Elmhadhbi, Mohamed-Hedi Karray, Bernard Archimède, and J. Neil Otte
    IEEE Transactions on Engineering Management 1-15. 2020.
    Disaster response is a highly collaborative and critical process that requires the involvement of multiple emergency responders (ERs), ideally working together under a unified command, to enable a rapid and effective operational response. Following the 9/11 and 11/13 terrorist attacks and the devastation of hurricanes Katrina and Rita, it is apparent that inadequate communication and a lack of interoperability among the ERs engaged on-site can adversely affect disaster response efforts. Within t…Read more