John Beverley

University at Buffalo
Johns Hopkins University Applied Physics Laboratory
  • University at Buffalo
    Department of Philosophy
    Assistant Professor
  • National Center for Ontological Research
    Administrator
  • Johns Hopkins University Applied Physics Laboratory
    Other (Part-time)
Northwestern University
Department of Philosophy
PhD, 2021
CV
Buffalo, NY, United States of America
  •  3855
    BFO: Basic Formal Ontology
    Applied ontology 17 (1): 17-43. 2022.
    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 repr…Read more
  •  3183
    The Infectious Disease Ontology in the Age of COVID-19
    with Shane Babcock, Lindsay G. Cowell, 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
  •  2608
    Speak No Evil: Understanding Hermeneutical (In)justice
    Episteme 19 (3): 431-454. 2022.
    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…Read more
  •  2495
    CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis
    with Oliver He, 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
  •  583
    Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology
    with Shane Babcock, Barry Smith, Yongqun He, Eric Merrell, Lindsay Cowell, Regina Hurley, and Sebastian Duesing
    Proceedings of the International Conference on Biomedical Ontologies. 2022.
    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) Co…Read more
  •  451
    Diverse Approaches to Meaning-Making at the End of Life
    with Hollen N. Reischer
    American Journal of Bioethics 19 (12): 68-70. 2019.
  •  438
    The Ties that Undermine
    Bioethics 30 (5): 304-311. 2015.
    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…Read more
  •  335
    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 judged to hav…Read more
  •  286
    Credibility Excess and Social Support Criterion
    with Hollen N. Reischer
    American Journal of Bioethics 19 (11): 32-34. 2019.
    Volume 19, Issue 11, November 2019, Page 32-34.
  •  269
    CIDO: The Community-Based Coronavirus Infectious Disease Ontology
    with Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-hui Huang, 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
  •  235
    A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
    with Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, 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, and Barry Smith
    Journal of Biomedical Semantics 13 (1): 25. 2022.
    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, integ…Read more
  •  232
    Careful What You Wish
    Philosophia 46 (1): 21-38. 2018.
    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 a…Read more
  •  228
    Responsibility Where We Find It
    Dissertation, Northwestern University. 2021.
    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 disposit…Read more
  •  197
    Book Review: Teaching Ethics - Modern Moral Philosophy (review)
    Teaching Ethics 20 1-2. 2020.
    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…Read more
  •  190
    A new framework for host-pathogen interaction research
    with Hong Yu, Li Li, Anthony Huffman, 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, and Yongqun He
    Frontiers in Immunology 13. 2022.
    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…Read more
  •  163
    A Critical Introduction to the Metaphysics of Time (review)
    Philosophy in Review 38 (3): 97-99. 2018.
  •  131
    ARGO: Arguments Ontology
    with Neil Otte, Francesco Franda, Brian Donohue, Alan Ruttenberg, Jean-Baptiste Guillion, and Yonatan Schreiber
    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…Read more
  •  125
    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. Successe…Read more
  •  121
    Grain of Salt
    In K. Vaidya (ed.), Teach Philosophy with a Sense of Humor. pp. 202-210. 2021.
    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 …Read more
  •  79
    Ontology Development Strategies and the Infectious Disease Ontology Ecosystem
    Proceedings of the International Conference on Biomedical Ontologies. 2023.
    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.
  •  57
    Coordinating virus research: The Virus Infectious Disease Ontology
    with Shane Babcock, Gustavo Carvalho, Lindsay G. Cowell, Sebastian Duesing, Yongqun He, Regina Hurley, Eric Merrell, Richard H. Scheuermann, and Barry Smith
    PLoS ONE 1. 2024.
    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 Biomed…Read more
  •  53
    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…Read more
  •  26
    Counternarrative Themes
    American Journal of Bioethics 21 (2): 72-74. 2021.
    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’...