• 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
  • 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’...
  • 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
  • A clear and provocative introduction to the ethics of COVID-19, suitable for university-level students, academics, and policymakers, as well as the general reader. It is also an original contribution to the emerging literature on this important topic. The author has made it available Open Access, so that it can be downloaded and read for free by all those who are interested in these issues. Key features include: A neat organisation of the ethical issues raised by the pandemic. An exploration of …Read more
  • 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
  • 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
  • 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
  • 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
  • Diverse Approaches to Meaning-Making at the End of Life
    Hollen N. Reischer and John Beverley
    American Journal of Bioethics 19 (12): 68-70. 2019.
  • Credibility Excess and Social Support Criterion
    John Beverley and Hollen N. Reischer
    American Journal of Bioethics 19 (11): 32-34. 2019.
    Volume 19, Issue 11, November 2019, Page 32-34.
  • The Ties that Undermine
    Bioethics 30 (5): 304-311. 2016.
    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
  • A Critical Introduction to the Metaphysics of Time (review)
    Philosophy in Review 38 (3): 97-99. 2018.
  • 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