With recent advancements in systems engineering and artificial intelligence, autonomous agents are increasingly being called upon to execute tasks that have normative relevance. These are tasks that directly—and potentially adversely—affect human well-being and demand of the agent a degree of normative-sensitivity and -compliance. Such norms and normative principles are typically of a social, legal, ethical, empathetic, or cultural (‘SLEEC’) nature. Whereas norms of this type are often framed in the abstract, or as high-level principles, addressing normative concerns in concrete applications (...) of autonomous agents requires the refinement of normative principles into explicitly formulated practical rules. This paper develops a process for deriving specification rules from a set of high-level norms, thereby bridging the gap between normative principles and operational practice. This enables autonomous agents to select and execute the most normatively favourable action in the intended context premised on a range of underlying relevant normative principles. In the translation and reduction of normative principles to SLEEC rules, we present an iterative process that uncovers normative principles, addresses SLEEC concerns, identifies and resolves SLEEC conflicts, and generates both preliminary and complex normatively-relevant rules, thereby guiding the development of autonomous agents and better positioning them as normatively SLEEC-sensitive or SLEEC-compliant. (shrink)

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 – (...) adequately addresses the injustice, and the accuracy of criticisms suggesting that Hermeneutical Justice is insufficient to the task. In what follows, after briefly defending necessary and sufficient conditions for what I take to be the best candidate interpretation of Hermeneutical Injustice, I build on recent work on moral responsibility to construct and defend a rigorous explication of Hermeneutical Justice. (shrink)

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 (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

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 (...) approaches to argument evaluation. Unlike most ontological approaches to arguments, ArgO utilizes Basic Formal Ontology (BFO) as an upper-level ontology, and may be used alongside other commonly used ontologies in the BFO framework, including boththe Information Artifact Ontology (IAO), and the Information Entity Ontology (INFO). Critically, our proposal is principled, based on rigorous definitions and formal axioms out of which characterizations of arguments naturally fall. It is our hope that ArgO may assist researchers in many projects, including: integrating heterogeneous sources of evidence, structuring the content of semantic wikis, and enhancing semantic reasoning. (shrink)

Volume 19, Issue 11, November 2019, Page 32-34.

This out-of-print collection in the area of European twentieth-century political philosophy includes selections from Adorno, Benjamin, Benhabib, Marcuse, Ciavatta, Comay, Honneth, and Fraser.

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 (...) with the construction of linear or partial ordering lists. Our two experiments suggest friction between priming and task, and also show once the priming tasks are cleared of potentially confounding semantic content, participants perform equally with respect to constructing linear or partial orders under similar priming conditions. (shrink)

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 (...) BFO framework. We provide discussion of these cases to provide a template for other ontologists using BFO, as well as to facilitate comparison with the strategies proposed by ontologists using different top-level ontologies. (shrink)

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 have a significant moral responsibility to donate tissue to a child conceived with his sperm, we think this will not be due to the fact that the donor stands in a close biological relationship to the recipient. Rather, we think such judgments will largely be grounded in the presumed unique ability of the sperm donor to help the child due to the compatibility of his tissues and organs with those of the recipient. In this paper, we report the results of two studies designed to investigate the comparative roles that biological relatedness and unique ability play in generating judgments of moral responsibility in tissue donation cases. We found that biologically related individuals are deemed to have a significant moral responsibility to donate tissue only when they are one of a small number of people who have the capacity to help. (shrink)

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 (...) of such scenarios. More specifically, I argue that sperm donor scenarios may be better explained by considering the unique abilities of agents involved. Appealing to unique ability does not eliminate the possibility of biological relations providing some explanation for perceived responsibilities on the part of biological fathers. However, since it is unclear exactly why biological relations are supposed to ground responsibility in the first place, and rather clear why unique ability grounds responsibility in those scenarios where it is exhibited, the burden of proof seems shifted to those advocating biological relations as grounds of responsibility to provide an explanation. Since this seems unlikely, I conclude it is best to avoid appealing to biological relations as providing grounds for responsibility. (shrink)

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 (...) to counterfactual attitudes which Ninan targets with his puzzle. In Section 2, I pose the counterfactual puzzle and present Ninan’s multi-centered world solution, emphasizing similarities and differences between multi-centered and centered world accounts of attitude reports. In Section 3, I argue the counterfactual attitude wishing falls under the purview of the multi-centered proposal, but that the proposal generates false predictions for wish reports concerning unsatisfiable content. I canvass responses, ultimately concluding Ninan’s proposal requires substantial revisions. (shrink)

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, (...) inaccuracy, and hallucinations, which underwrite concerns over the reliability and trustworthiness of these systems, motivating investigations into commonsense reasoning, AI explainability, and formal verification techniques. Moreover, proper assessments of hybrid machine learning/symbolic systems require novel strategies to facilitate comparisons of performance and guide future AI progress. The EDGeS AAAI 2023 Spring symposium brought together researchers focusing on novel assessments and benchmarks for evaluating hybrid and artificial general intelligence (AGI) systems. This symposium revealed what was already suspected: research concerning evaluation of machine learning/symbolic hybrids and AGI is, unfortunately, lacking. Even so, the discussion was fruitful. (shrink)

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 (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

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! (...) I counted equivocations over use/mention, identity/predication, measurements, and lexical/material parthood, but I’m sure there are more hiding. -/- If you share my interest in untangling these errors, I’ve copied Carroll’s dialogue below. I’ve found the task best pursued with help, whether students, interns, sisters, tarot readers, etc. As you’ll see, I’ve divided the dialogue into five sections, of varying difficulties. I recommend dividing helpers accordingly, assigning one section per group, then directing each to identify both good and bad reasoning in the section. After some time, groups should pass their discoveries to other groups for scrutiny. For example, if group 1 examined section 1, they’d pass their discoveries to group 2 who then checks group 1’s work against section 1. Proceed until each group has examined each section and – hopefully – you’ll find all the errors. Happy hunting! (shrink)

This paper examines the role of ?situations? in John Dewey's philosophy of logic. To do this properly it is necessary to contrast Dewey's conception of experience and mentality with views characteristic of modern epistemology. The primary difference is that, rather than treat experience as peripheral and or external to mental functions (reason, etc.), we should treat experience as a field in and as a part of which thinking takes place. Experience in this broad sense subsumes theory and fact, hypothesis and (...) evidence, reason and observation, thought and perception. Logic in this view is a formal study of the generic features of all possible kinds of experience in this broad (thick, deep, wide, multifaceted) sense. The goal of this paper is to explain what Dewey thinks a situation is in the context of this view of experience, and to argue for the fundamental importance of that idea for logic and philosophy in general. (shrink)

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 (...) that are themselves often refined into more sophisticated dispositions to infer as we develop. Given how foundational such know-how is to our understanding of the world, we find ourselves responsible for cultivating more sophisticated reasoning, whatever its provenance. In the chapter Ties that Undermine, I argue attributions to an agent of moral responsibility are largely influenced by the perceived rareness of that agent's ability to provide aid or prevent harm, degree of aid provided or harm prevented, and cost to that agent in providing aid or preventing harm. Voluntary adoption of such moral responsibility is not necessary for an agent to be morally responsible. I generalize this result to the epistemic domain in the chapter Speak No Evil: Understanding Hermeneutical (In)justice, arguing attributions to an agent of epistemic responsibility are also influenced by the perceived rareness of that agent's ability to generate true beliefs in themselves and others, extent of benefit provided and harm prevented by having such true beliefs, and cost to that agent in generating such true beliefs. Here, we see voluntary adoption of such epistemic responsibility is not necessary for an agent to be epistemically responsible. By exploring the relevance of such responsibility to three distinct debates in three distinct sub-fields of philosophy, this dissertation highlights how pervasive responsibility is to the lives of agents, and the work of philosophers. (shrink)

This article offers a novel, conservative account of material constitution, one that incorporates sortal essentialism and features a theory of dominant sortals. It avoids coinciding objects, temporal parts, relativizations of identity, mereological essentialism, anti-essentialism, denials of the reality of the objects of our ordinary ontology, and other departures from the metaphysic implicit in ordinary ways of thinking. Defenses of the account against important objections are found in Burke 1997, 2003, and 2004, as well as in the often neglected six (...) paragraphs that conclude section V of this article. (shrink)

This collection in the area of continental philosophy of language, aesthetics, and semiotics includes articles and book selections from Derrida, Ricouer, McCumber, Oliver, Sheshradi-Krooks, Lacan, and Kristeva. This collection is available in the University of Guelph bookstore.

This collection of writings on aesthetics includes selections from Theodor Adorno, Walter Benjamin, Mikhail Bakhtin, Sigmund Freud, Martin Heidegger, Amy Mullin, Friedrich Nietzsche, and Frederich Wilhelm Joseph von Schelling. This collection may still be available as a print-on-demand title at the Ryerson University bookstore.

This collection for a course in Social Thought and the Critique of Power includes selections from Sandra Bartkey, Wendy Brown, Judith Butler, Luc Boltanski, Eve Chiapello, Juergin Habermas, Margaret Kohn, Saskia Sassen, Margit Mayer, David Ciavatta, Michael Hardt, Antonio Negri, and Jeremy Waldron. Selections include material on the city, neoliberalism, computer-mediated life, precarity, cosmopolitanism, and gender. This packet may still be available as a print-on-demand title at the Ryerson University Bookstore.

This out-of-print collection on animal rights, applied ethics, and continental philosophy includes readings by Martin Heidegger, Karin De Boer, Martha Nussbaum, David De Grazia, Giorgio Agamben, Peter Singer, Tom Regan, David Morris, Michael Thompson, Stephen Jay Gould, Sue Donaldson, Carolyn Merchant, and Jacques Derrida.

This out-of-print, two-volume, photocopy packet, in the area of "Surrealism and the Politics of the Particular" includes readings on language, meaning, and surrealism from Adorno, Benjamin, McCumber, Breton, Heidegger, Freud, Kristeva, Ricouer, and Bataille.

This out-of-print collection in the area of the history, politics, ethics, and theory of privacy includes selections from Peter Gay, Alan Westin, Walter Benjamin, Catharine MacKinnon, Seyla Benhabib, Anita Allen, Ann Jennings, Charles Taylor, Richard Sennett, Mark Wicclair, Martha Nussbaum, and Robert Nozick.

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, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

On the most popular account of material constitution, it is common for a material object to coincide precisely with one or more other material objects, ones that are composed of just the same matter but differ from it in sort. I argue that there is nothing that could ground the alleged difference in sort and that the account must be rejected.

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.

Dion is a full-bodied man. Theon is that part of him which consists of all of him except his left foot. What becomes of Dion and Theon when Dion’s left foot is amputated? Employing the doctrine of sortal essentialism, I defend a surprising answer last defended by Chrysippus: that Dion survives while the seemingly unscathed Theon perishes. For replies to critics, see my publications of 1997 and (especially) 2003.

It is hard to see why the head and other brain-containing parts of a person are not themselves persons, or at least thinking, conscious beings. Some theorists have sought to reconcile us to the existence of thinking person-parts. Others have sought to avoid them but have relied on radical theories at odds with the metaphysic implicit in ordinary ways of thinking. This paper offers a novel, conservative solution, one on which the heads and other brain-containing parts of persons do exist (...) but are neither persons, thinkers, nor conscious beings. A much briefer statement of the solution is found in section 5 of Burke 2004. (shrink)

Dion is a full-bodied man. Theon is that part of him which consists of all of him except his left foot. What becomes of Dion and Theon when Dion’s left foot is amputated? In Burke 1994, employing the doctrine of sortal essentialism, I defended a surprising position last defended by Chrysippus: that Dion survives while the seemingly unscathed Theon perishes. This paper defends that position against objections by Stone, Carter, Olson, and others. Most notably, it offers a novel, conservative (...) solution to the many-thinkers problem, a solution that enables us to accept the existence of brain-containing person-parts while denying that those person-parts are thinking, conscious beings. (shrink)

This is the introduction to the inaugural issue of The Journal of Philosophy of Disability.

Suppose that five minutes ago, to our astonishment, a healthy, full-grown duck suddenly popped into existence on the table in front of us. Suppose further that there was no first time at which the duck existed but rather a last time, T, at which it had yet to exist. Then for each time t at which the duck has existed, there is an explanation of why the duck existed at t: there was a time t’ earlier than t but later (...) than T such that the duck existed at t’, and it was only to be expected that a healthy duck would survive the brief period from t’ to t. But would these explanations remove the mystery? Taken collectively, would they explain why the duck has existed since T rather than never having existed at all? Presumably not. But if not, this seems to discredit the style of explanation offered by Hume and Edwards for the infinite regress they hypothesize of causes and effects. (shrink)

Mobile phones are reportedly the most rapidly expanding e-reading device worldwide. However, the embodied, cognitive and affective implications of smartphone-supported fiction reading for leisure (m-reading) have yet to be investigated empirically. Revisiting the theoretical work of digitization scholar Anne Mangen, we argue that the digital reading experience is not only contingent on patterns of embodied reader–device interaction (Mangen, 2008 and later) but also embedded in the immediate environment and broader situational context. We call this the situation constraint. Its application to (...) Mangen’s general framework enables us to identify four novel research areas, wherein m-reading should be investigated with regard to its unique affordances. The areas are reader–device affectivity, situated embodiment, attention training and long-term immersion. (shrink)

The “staccato run,” in which a runner stops infinitely often while running from one point to another, is a prototypical “superfeat,” that is, a feat involving the completion in a finite time of an infinite sequence of distinct acts. There is no widely accepted demonstration that superfeats are impossible logically, but I argue here, contra Grunbaüm, that they are impossible dynamically. Specifically, I show that the staccato run is excluded by Newton’s three laws of motion, when those laws are supplemented (...) with a defensible philosophical judgment. (shrink)

(The downloadable document, posted 07/23/22, incorporates post-publication corrections/refinements, mainly of section II.) The article gives a novel argument to show that there is sense of 'exists' suitable for posing a substantive issue between presentists and eternalists. It then seeks to invigorate a neglected variety of presentism. There are seven doctrines, widely accepted even among presentists, that create problems for presentism. Without distinguishing existence and being, presentists can comfortably reject all seven. Doing so would dispose of the majority of presentism’s problems. (...) Further, it would enable presentists to reduce A-judgments to B-judgments, thereby insulating presentism from doubts about the intelligibility of A-theories. For reasons indicated very briefly, it might also make presentism less difficult to reconcile with special relativity, though the point is not pursued here. (shrink)

The objective of this article is to review extant empirical studies of empathy in narrative reading in light of (i) contemporary literary theory, and (ii) neuroscientific studies of empathy, and to discuss how a closer interplay between neuroscience and literary studies may enhance our understanding of empathy in narrative reading. An introduction to some of the philosophical roots of empathy is followed by tracing its application in contemporary literary theory, in which scholars have pursued empathy with varying degrees of conceptual (...) precision, often within the context of embodied/enactive cognition. The presentation of empirical literary studies of empathy is subsequently contextualized by an overview of psychological and neuroscientific aspects of empathy. Highlighting points of convergence and divergence, the discussion illustrates how findings of empirical literary studies align with recent neuroscientific research. The article concludes with some prospects for future empirical research, suggesting that digitization may contribute to advancing the scientific knowledge of empathy in narrative reading. (shrink)

This paper compares Dewey's and Russell's views of "immediate knowledge." Dewey was perhaps mistaken in attributing to Russell the view that immediate sense data provide incorrigible foundations for knowledge. Russell's characterization of sensing plus attention as the most immediate knowing of which we have experience nevertheless remains a valid target of Dewey's criticisms. These two philosophers developed very different theories of logic and knowledge, language and experience. Given the reconstructed notions of experience and knowledge at the root of Dewey's logical (...) theory, referring to knowledge as immediate or nearly immediate constitutes a serious category mistake. (shrink)

This paper examines the settlement movement (a social reform movement during the Progressive Era, roughly 1890–1920) in order to illustrate what pragmatism is and is not. In 1906, Mary Kingsbury Simkhovitch proposed an analysis of settlement house methods. Because of her emphasis on interpretation and action, and because of the nature of the settlement movement as a social reform effort with vitally important consequences for everyone involved, it might be thought that her analysis would be pragmatist in character. This paper (...) shows that her analysis is empiricist, not pragmatist, and offers an alternative pragmatist sketch of settlement house methodology. (shrink)

The limited aim here is to explain what John Dewey might say about the formulation of the grue example. Nelson Goodman’s problem of distinguishing good and bad inductive inferences is an important one, but the grue example misconstrues this complex problem for certain technical reasons, due to ambiguities that contemporary logical theory has not yet come to terms with. Goodman’s problem is a problem for the theory of induction and thus for logical theory in general. Behind the whole discussion of (...) these issues over the last several decades is a certain view of logic hammered out by Russell, Carnap, Tarski, Quine, and many others. Goodman’s nominalism hinges in essential ways on a certain view of formal logic with an extensional quantification theory at its core. This raises many issues, but the one issue most germane here is the conception of predicates ensconced in this view of logic. (shrink)

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 (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

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 (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

People are increasingly exposed to conflicting health information and must navigate this information to make numerous decisions, such as which foods to consume, a process many find difficult. Although some consumers attribute these disagreements to aspects related to uncertainty and complexity of research, many use a narrower set of credibility-based explanations. Experts’ views on disagreements are underinvestigated and lack explicit identification and classification of the differences in causes for disagreement. Consequently, there is a gap in existing literature to understand the (...) range of reasons for these contradictions. Combining the findings from a literature study and expert interviews, a taxonomy of disagreements was developed. It identifies 10 types of disagreement classified under three dimensions: informant-, information- and uncertainty-related causes for disagreement. The taxonomy may assist with adoption of more effective strategies to deal with conflicting information and contributes to research and practice of science communication in the context of disagreement. (shrink)

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 initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

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.

WHO in 2019 established the Advisory Committee on Developing Global Standards for Governance and Oversight of Human Genome Editing, which has recently published a Draft Governance Framework on Human Genome Editing. Although the Draft Framework is a good point of departure, there are four areas of concern: first, it does not sufficiently address issues related to establishing safety and efficacy. Second, issues that are a source of tension between global standard setting and state sovereignty need to be addressed in a (...) more nuanced fashion. Third, it fails to meaningfully engage with the extent to which the conceptualisation of human dignity may justifiably vary between jurisdictions. Fourth, the meaning of harm to the interests of a future person requires clarity. Provided these four areas of concern can be addressed, the future of the global governance of human genome editing may hold promise. (shrink)

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 (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

Good old-fashioned cognitive science characterizes human thinking as symbol manipulation qua computation and therefore emphasizes the processing of symbolic representations as a necessary if not sufficient condition for “general intelligent action.” Recent alternative conceptions of human thinking tend to deemphasize if not altogether eschew the notion of representation. The present paper shows how classical American pragmatist conceptions of human thinking can successfully avoid either of these extremes, replacing old-fashioned conceptions of representation with one that characterizes both representatum and representans in (...) externalist terms. (shrink)