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John Beverley
University at Buffalo
  1. Speak No Evil: Understanding Hermeneutical (In)justice.John Beverley - 2022 - Episteme 19 (3):431-454.
    Miranda Fricker's original presentation of Hermeneutical Injustice left open theoretical choice points leading to criticisms and subsequent clarifications with the resulting dialectic appearing largely verbal. The absence of perspicuous exposition of hallmarks of Hermeneutical Injustice might suggest scenarios exhibiting some – but not all – such hallmarks are within its purview when they are not. The lack of clear hallmarks of Hermeneutical Injustice, moreover, obscures both the extent to which Fricker's proposed remedy Hermeneutical Justice – roughly, virtuous communicative practices – (...)
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  2. BFO: Basic Formal Ontology.J. Neil Otte, John Beverley & Alan Ruttenberg - 2022 - Applied ontology 17 (1):17-43.
    Basic Formal Ontology (BFO) is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined classes, and relations employing the (...)
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  3. A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian Athey & Barry Smith - 2022 - Journal of Biomedical Semantics 13 (1):25.
    The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...)
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  4. ARGO: Arguments Ontology.John Beverley, Neil Otte, Francesco Franda, Brian Donohue, Alan Ruttenberg, Jean-Baptiste Guillion & Yonatan Schreiber - manuscript
    Although the last decade has seen a proliferation of ontological approaches to arguments, many of them employ ad hoc solutions to representing arguments, lack interoperability with other ontologies, or cover arguments only as part of a broader approach to evidence. To provide a better ontological representation of arguments, we present the Arguments Ontology (ArgO), a small ontology for arguments that is designed to be imported and easily extended by researchers who work in different upper-level ontology frameworks, different logics, and different (...)
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  5. The Infectious Disease Ontology in the Age of COVID-19.Shane Babcock, Lindsay G. Cowell, John Beverley & Barry Smith - 2021 - Journal of Biomedical Semantics 12 (13).
    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 pathogens. In this paper we (...)
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  6. Judgments of moral responsibility in tissue donation cases.John Beverley & James Beebe - 2017 - Bioethics 32 (2):83-93.
    If a person requires an organ or tissue donation to survive, many philosophers argue that whatever moral responsibility a biological relative may have to donate to the person in need will be grounded at least partially, if not entirely, in biological relations the potential donor bears to the recipient. We contend that such views ignore the role that a potential donor's unique ability to help the person in need plays in underwriting such judgments. If, for example, a sperm donor is (...)
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  7. 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 & Hong Yu - 2020 - Scientific Data 181 (7):5.
    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), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...)
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  8.  39
    Coordinating virus research: The Virus Infectious Disease Ontology.John Beverley, Shane Babcock, Gustavo Carvalho, Lindsay G. Cowell, Sebastian Duesing, Yongqun He, Regina Hurley, Eric Merrell, Richard H. Scheuermann & Barry Smith - 2024 - PLoS ONE 1.
    The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...)
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  9. The Ties that Undermine.John Beverley - 2015 - Bioethics 30 (5):304-311.
    Do biological relations ground responsibilities between biological fathers and their offspring? Few think biological relations ground either necessary or sufficient conditions for responsibility. Nevertheless, many think biological relations ground responsibility at least partially. Various scenarios, such as cases concerning the responsibilities of sperm donors, have been used to argue in favor of biological relations as partially grounding responsibilities. In this article, I seek to undermine the temptation to explain sperm donor scenarios via biological relations by appealing to an overlooked feature (...)
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  10.  46
    Semantic Priming on Ordering Tasks.John Beverley & Nate Lauffer - manuscript
    Moeser suggested participants default to linear ordering elements but they can be primed to impose either linear or partial ordering. This study seems problematic insofar as ‘greater than’ might be understood to incline participants to favor linear orderings. Recent follow-up studies strongly suggest participants do not default to linear ordering. It seems plausible, moreover, that the observed priming effect is far more pervasive than Moeser countenanced. The present work explores the extent to which priming for linear or partial orders conflicts (...)
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  11.  54
    Ontology Development Strategies and the Infectious Disease Ontology Ecosystem.Giacomo De Colle, Ali Hasanzadeh & John Beverley - 2023 - Proceedings of the International Conference on Biomedical Ontologies.
    After motivating a framework for evaluating top-down, middle-out, middle-in, and bottom-up ontology development strategies, we apply our framework to investigate whether infectious disease ontologies - specifically, the Virus Infectious Disease Ontology (VIDO) and the Coronavirus Infectious Disease Ontology (CIDO) - effectively promote semantic interoperability.
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  12. Evaluation and Design of Generalist Systems (EDGeS).John Beverley & Amanda Hicks - 2023 - Ai Magazine.
    The field of AI has undergone a series of transformations, each marking a new phase of development. The initial phase emphasized curation of symbolic models which excelled in capturing reasoning but were fragile and not scalable. The next phase was characterized by machine learning models—most recently large language models (LLMs)—which were more robust and easier to scale but struggled with reasoning. Now, we are witnessing a return to symbolic models as complementing machine learning. Successes of LLMs contrast with their inscrutability, (...)
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  13. Credibility Excess and Social Support Criterion.John Beverley & Hollen N. Reischer - 2019 - American Journal of Bioethics 19 (11):32-34.
    Volume 19, Issue 11, November 2019, Page 32-34.
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  14. Careful What You Wish.John Beverley - 2018 - Philosophia 46 (1):21-38.
    Dilip Ninan has raised a puzzle for centered world accounts of de re attitude reports extended to accommodate what he calls “counterfactual attitudes.” As a solution, Ninan introduces multiple centers to the standard centered world framework, resulting in a more robust semantics for de re attitude reports. However, while the so-called multi-centered world proposal solves Ninan’s counterfactual puzzle, this additional machinery is not without problems. In Section 1, I present the centered world account of attitude reports, followed by the extension (...)
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  15. A new framework for host-pathogen interaction research.Hong Yu, Li Li, Anthony Huffman, John Beverley, Junguk Hur, Eric Merrell, Hsin-hui Huang, Yang Wang, Yingtong Liu, Edison Ong, Liang Cheng, Tao Zeng, Jingsong Zhang, Pengpai Li, Zhiping Liu, Zhigang Wang, Xiangyan Zhang, Xianwei Ye, Samuel K. Handelman, Jonathan Sexton, Kathryn Eaton, Gerry Higgins, Gilbert S. Omenn, Brian Athey, Barry Smith, Luonan Chen & Yongqun He - 2022 - Frontiers in Immunology 13.
    COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...)
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  16. Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology.John Beverley, Shane Babcock, Barry Smith, Yongqun He, Eric Merrell, Lindsay Cowell, Regina Hurley & Sebastian Duesing - 2022 - Proceedings of the International Conference on Biomedical Ontologies.
    The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...)
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  17. Diverse Approaches to Meaning-Making at the End of Life.Hollen N. Reischer & John Beverley - 2019 - American Journal of Bioethics 19 (12):68-70.
  18. Grain of Salt.John Beverley - 2021 - In K. Vaidya (ed.), Teach Philosophy with a Sense of Humor. pp. 202-210.
    Imagine my surprise at discovering - tucked inside the cover of a first edition Alice in Wonderland – an unknown dialogue written by Lewis Carroll himself! It was scribbled on the back of a napkin, punctuated by Carroll’s tell-tale signature, and seems to have been written hastily. Carroll is known among laypersons as an absurdist, but he’s esteemed among formal thinkers as impressively logical. You can probably then imagine my further surprise at discovering various fallacies and confusions in the dialogue! (...)
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  19.  9
    The Postmodernism Debate in Latin America.John Beverley, Michael Aronna & José Oviedo - 1995 - Duke University Press.
    Postmodernism may seem a particularly inappropriate term when used in conjunction with a region that is usually thought of as having only recently, and then unevenly, acceded to modernity. Yet in the last several years the concept has risen to the top of the agenda of cultural and political debate in Latin America. This collection explores the Latin American engagement with postmodernism, less to present a regional variant of the concept than to situate it in a transnational framework. Recognizing that (...)
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  20.  25
    Counternarrative Themes.John Beverley & Regina Hurley - 2021 - American Journal of Bioethics 21 (2):72-74.
    Mithani et al. argue that bioethics should more actively resist racial injustice and expand the range of voices heard beyond those historically considered. We largely agree with the authors’...
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  21. Responsibility Where We Find It.John Beverley - 2021 - Dissertation, Northwestern University
    There is more responsibility on heaven and earth than dreamt of in most philosophy. This dissertation explores three debates in three sub-fields of philosophy, highlighting in each responsibilities agents find themselves with whether they like it or not. In the chapter "Trust Logic, Not Tortoises", I propose an answer to Wright’s Justification Question – to what extent are we justified in our knowledge of logic? – arguing early knowledge of logic is a species of know-how underwritten by dispositions to infer (...)
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  22.  39
    These Are the Times We Have to Live in: An Interview with Roberto Fernández Retamar.Goffredo Diana, John Beverley & Roberto Fernández Retamar - 1995 - Critical Inquiry 21 (2):411-433.
  23. Book Review: Teaching Ethics - Modern Moral Philosophy. [REVIEW]John Beverley - 2020 - Teaching Ethics 20:1-2.
    Daniel R. DeNicola’s Moral Philosophy: A Contemporary Introduction begins (pg. ix) with an anonymous reviewer’s quote, paraphrased here: ‘The author of an introductory ethics textbook has an impossible task, creating a work both accessible to undergraduates and rigorous enough for philosophers.’ DeNicola can of course be forgiven for not achieving this impossible task. Still, some attempts are better than others. After surveying the text content, I explain why I discourage instructors from using this textbook in introductory ethics courses.
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  24. A Critical Introduction to the Metaphysics of Time. [REVIEW]John Beverley - 2018 - Philosophy in Review 38 (3):97-99.
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  25. Facts in logical space: A tractarian ontology Jason Turner oxford: Oxford university press, 2016; 362 pp.; $85.00. [REVIEW]John Beverley - 2018 - Dialogue 57 (3):637-639.
  26.  14
    Situating Knowledges: Latin American Readings of PostmodernismThe Postmodernism Debate in Latin AmericaPostmodernism: Center and PeripheryOn Edge. The Crisis of Contemporary Latin American Culture. [REVIEW]Laura Garcia-Moreno, John Beverley, Jose Oviedo, Desiderio Navarro, George Yudice, Jean Franco & Juan Flores - 1995 - Diacritics 25 (1):63.
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