John Beverley

John Beverley
University at Buffalo, State University of New York | SUNY Buffalo · Department of Philosophy

Doctor of Philosophy

About

39
Publications
11,535
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381
Citations
Introduction
I'm presently: (1) Developing logically well-structured vocabularies covering the domain of viruses in general and SARS-CoV-2 in particular; (2) Developing an analysis of epistemic/moral responsibility, supported empirically, generating prescriptions in a range of use cases; (3) Building a class of modal logics with inverted accessibility relations, and embeddings into existing modal structures; (4) Investigating pedagogy strategies. See https://johnbeverley.com/

Publications

Publications (39)
Chapter
The Common Core Ontologies(CCO) are designed as a mid-level ontology suite that extends the Basic Formal Ontology. In 2017,CUBRC, Inc. made CCO openly available. CCO has since been increasingly adopted by a broad group of users and applications and is proposed as the first standard mid-level ontology. Despite these successes, documentation of the c...
Article
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Background Within the Open Biological and Biomedical Ontology (OBO) Foundry, many ontologies represent the execution of a plan specification as a process in which a realizable entity that concretizes the plan specification, a “realizable concretization” (RC), is realized. This representation, which we call the “RC-account”, provides a straightforwa...
Preprint
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The Provenance Ontology (PROV-O) is a World Wide Web Consortium (W3C) recommended ontology used to structure data about provenance across a wide variety of domains. Basic Formal Ontology (BFO) is a top-level ontology ISO/IEC standard used to structure a wide variety of ontologies, such as the OBO Foundry ontologies and the Common Core Ontologies (C...
Preprint
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This paper introduces a set of terms that are intended to act as an interface between cyber ontologies (like a file system ontology or a data fusion ontology) and top- and mid-level ontologies, specifically Basic Formal Ontology and the Common Core Ontologies. These terms center on what makes cyberinformation management unique: numerous acts of cop...
Preprint
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Generative artificial intelligence (AI), exemplified by the release of GPT-3.5 in 2022, has significantly advanced the potential applications of large language models (LLMs), including in the realms of ontology development and knowledge graph creation. Ontologies, which are structured frameworks for organizing information, and knowledge graphs, whi...
Article
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 interop...
Article
Full-text available
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. Thi...
Preprint
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 Argument...
Conference Paper
Full-text available
The Occupation Ontology (OccO) is a community-based ontology for occupations, which extends from the upper-level Basic Formal Ontology (BFO) in accordance with Open Biological and Biomedical (OBO) Foundry principles. In this article, we report on updates to core OccO definitions after expanding representational coverage to include codes from US SOC...
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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 interacti...
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Background 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 lar...
Article
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...
Article
Full-text available
Ontologies have emerged to become critical to support data and knowledge representation, standardization, integration, and analysis. The SARS-CoV-2 pandemic led to the rapid proliferation of COVID-19 data, as well as the development of many COVID-19 ontologies. In the interest of supporting data interoperability, we initiated a community-based effo...
Article
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Background Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool, and this holds especially for those ontologies built on the design principles of the Open Biomedical Ontologies Foundry. These p...
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Examines a model for respectful engagement with counter-narratives by individuals unfamiliar with those narratives, using the resources of narrative identity theory.
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Critical review of DeNicola's "Moral Philosophy - A Contemporary Introduction." In brief, I do not recommend. Despite the title, it is neither contemporary nor an introduction, and provides false impressions as to what moral philosophy is.
Chapter
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Recently 'discovered' dialogue hastily written by Lewis Carroll, full of subtle fallacies and melodic confusions. Useful for teaching students introductory critical thinking concepts. Includes a key.
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The Coronavirus Infectious Disease Ontology (CIDO) is a community-based ontology that supports coronavirus disease knowledge and data standardization, integration, sharing, and analysis.
Article
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 h...
Conference Paper
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 dr...
Preprint
Full-text available
The COVID-19 pandemic prompted immense investigation of the SARS-CoV-2 virus. 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...
Preprint
Full-text available
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 Argument...
Preprint
Full-text available
I examine Kripke and Padro’s recent result that basic rules of logic - such as universal instantiation - cannot be adopted, and apply this lesson to two extant answers to the Justification Question, i.e. how are basic rules of logic justified? One answer was provided by Carnap’s doctrine of logical conventionalism; another by Quine’s holism. I argu...
Preprint
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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....
Preprint
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There are independent reasons for expanding the sorts of contents expressed by various sentence types with respect to logics and there are independent reasons for distinguishing among syntactic entities that generate varieties of reference failure. What is perhaps not obvious, however, is how accepting these constraints addresses the disease that i...
Preprint
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I extract and refine a detailed characterization of a very commonly discussed approach to understanding epistemic injustices. I supplement that approach with an analysis of moral and epistemic responsibility, and apply this analysis to several cases to demonstrate accuracy.
Preprint
Full-text available
Background Efforts to respond effectively to public health emergencies, such as we are now experiencing with COVID-19, require data sharing across multiple disciplines, and this is hindered by the fact that relevant information is often collected using discipline-specific terminologies and coding systems and stored in heterogenous databases. Ontolo...
Preprint
Full-text available
As we move forward in our efforts to refine the IDO suite, many of the IDO extensions will require reengineering. Here we detail some of the issues that need to be addressed within specific IDO extensions. Note*: this unpublished manuscript is intended as a supplement for our preprint article “The Infectious Disease Ontology in the Age of Covid-19...
Article
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The U.S. population is rapidly aging. Personality psychologists have paid relatively little attention to personality at the end of life, a time of marked shifts in social roles and increases in individual contemplation. Narrative identity theory, one of the newer foci of personality research, seems particularly poised to do such research as it emph...
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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-centere...
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Facts in Logical Space: A Tractarian Ontology JASON TURNER Oxford: Oxford University Press, 2016; 362 pp.; $85.00 (hardcover) - JOHN BEVERLEY
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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 th...
Article
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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 o...

Questions

Questions (3)
Question
In my early education I was taught radioactive decay was - in general - not affected by environmental variables. This seems to have been disputed in recent years. I'm curious about the current state of the debate. Are there good reasons to think radioactive decay rates are affected by environmental variables?
Question
Seriality on certain modal frames - that for every world w there is some world v such that wRv - corresponds to the axiom: ◻P→♢P, assuming a standard interpretation of the relevant operators. Consider what we might call reverse seriality: that for every world w there is some world v such that vRw.
Is there an axiom to which reverse seriality corresponds, assuming a standard interpretation of the operators? I've observed any frame satisfying reflexivity, i.e. every w is such that wRw which corresponds to the axiom: ◻P →P, satisfies reverse seriality, but I've gotten no further on the answer.
(P.S. If this is a 'good question' let me relay that I heard it from a student who took a course with Sean Ebel-Duggan who posed it; on the other hand, if this is a 'bad question' then it's likely due to my or the student's misunderstanding of Sean's actual question).

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