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 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)

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)

Inspired by Rudolf Carnap's Der Logische Aufbau Der Welt, David J. Chalmers argues that the world can be constructed from a few basic elements. He develops a scrutability thesis saying that all truths about the world can be derived from basic truths and ideal reasoning. This thesis leads to many philosophical consequences: a broadly Fregean approach to meaning, an internalist approach to the contents of thought, and a reply to W. V. Quine's arguments against the analytic and the a (...) priori. Chalmers also uses scrutability to analyze the unity of science, to defend a conceptual approach to metaphysics, and to mount a structuralist response to skepticism. Based on the 2010 John Locke lectures, Constructing the World opens up debate on central philosophical issues involving language, consciousness, knowledge, and reality. This major work by a leading philosopher will appeal to philosophers in all areas. This entry contains uncorrected proofs of front matter, chapter 1, and first excursus. (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)

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)

[This is an edited version of a keynote talk at the conference on Neural Information Processing Systems (NeurIPS) on November 28, 2022, with some minor additions and subtractions.] -/- There has recently been widespread discussion of whether large language models might be sentient or conscious. Should we take this idea seriously? I will break down the strongest reasons for and against. Given mainstream assumptions in the science of consciousness, there are significant obstacles to consciousness in current models: for example, their (...) lack of recurrent processing, a global workspace, and unified agency. At the same time, it is quite possible that these obstacles will be overcome in the next decade or so. I conclude that while it is somewhat unlikely that current large language models are conscious, we should take seriously the possibility that successors to large language models may be conscious in the not-too-distant future. (shrink)

Does consciousness collapse the quantum wave function? This idea was taken seriously by John von Neumann and Eugene Wigner but is now widely dismissed. We develop the idea by combining a mathematical theory of consciousness (integrated information theory) with an account of quantum collapse dynamics (continuous spontaneous localization). Simple versions of the theory are falsified by the quantum Zeno effect, but more complex versions remain compatible with empirical evidence. In principle, versions of the theory can be tested by experiments with (...) quantum computers. The upshot is not that consciousness-collapse interpretations are clearly correct, but that there is a research program here worth exploring. (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)

This paper offers both a theoretical and an experimental perspective on the relationship between connectionist and Classical (symbol-processing) models. Firstly, a serious flaw in Fodor and Pylyshyn’s argument against connectionism is pointed out: if, in fact, a part of their argument is valid, then it establishes a conclusion quite different from that which they intend, a conclusion which is demonstrably false. The source of this flaw is traced to an underestimation of the differences between localist and distributed representation. It has (...) been claimed that distributed representations cannot support systematic operations, or that if they can, then they will be mere implementations of traditional ideas. This paper presents experimental evidence against this conclusion: distributed representations can be used to support direct structure-sensitive operations, in a man- ner quite unlike the Classical approach. Finally, it is argued that even if Fodor and Pylyshyn’s argument that connectionist models of compositionality must be mere implementations were correct, then this would still not be a serious argument against connectionism as a theory of mind. (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)

There are two versions of the language-of-thought hypothesis (LOT): Representational LOT (roughly, structured representation), introduced by Ockham, and computational LOT (roughly, symbolic computation) introduced by Fodor. Like many others, I oppose the latter but not the former. Quilty-Dunn et al. defend representational LOT, but they do not defend the strong computational LOT thesis central to the classical-connectionist debate.

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)

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)

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)

Conceptual engineering is the design, implementation, and evaluation of concepts. Conceptual engineering includes or should include de novo conceptual engineering (designing a new concept) as well as conceptual re-engineering (fixing an old concept). It should also include heteronymous (different-word) as well as homonymous (same-word) conceptual engineering. I discuss the importance and the difficulty of these sorts of conceptual engineering in philosophy and elsewhere.

Cartesian arguments for global skepticism about the external world start from the premise that we cannot know that we are not in a Cartesian scenario such as an evil-demon scenario, and infer that because most of our empirical beliefs are false in such a scenario, these beliefs do not constitute knowledge. Veridicalist responses to global skepticism respond that arguments fail because in Cartesian scenarios, many or most of our empirical beliefs are true. Some veridicalist responses have been motivated using verificationism, (...) externalism, and coherentism. I argue that a more powerful veridicalist response to global skepticism can be motivated by structuralism, on which physical entities are understood as those that play a certain structural role. I develop the structuralist response and address objections. (shrink)

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)

Abstract The explosion of interest in large language models (LLMs) has been accompanied by concerns over the extent to which generated outputs can be trusted, owing to the prevalence of bias, hallucinations, and so forth. Accordingly, there is a growing interest in the use of ontologies and knowledge graphs to make LLMs more trustworthy. This rests on the long history of ontologies and knowledge graphs in constructing human-comprehensible justification for model outputs as well as traceability concerning the impact of evidence (...) on other evidence. Understanding the nature of arguments and argumentation is critical to each, especially when LLM output conflicts with what is expected by users. The central contribution of this article is to extend the Arguments Ontology (ARGO) - an ontology specific to the domain of argumentation and evidence broadly construed - into the space of LLM fact-checking in the interest of promoting justification and traceability research through the use of ARGO-based ‘blueprints’. (shrink)

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

What are the philosophical views of contemporary professional philosophers? We surveyed many professional philosophers in order to help determine their views on 30 central philosophical issues. This article documents the results. It also reveals correlations among philosophical views and between these views and factors such as age, gender, and nationality. A factor analysis suggests that an individual's views on these issues factor into a few underlying components that predict much of the variation in those views. The results of a metasurvey (...) also suggest that many of the results of the survey are surprising: philosophers as a whole have quite inaccurate beliefs about the distribution of philosophical views in the profession. (shrink)

Mid-level ontologies are used to integrate data across disparate domains using vocabularies more specific than top-level ontologies and more general than domain-level ontologies. There are no clear, defensible criteria for determining whether a given ontology should count as mid-level, because we lack a rigorous characterization of what the middle level of generality is supposed to contain. Attempts to provide such a characterization have failed, we believe, because they have focused on the goal of specifying what is characteristic of those single (...) ontologies that have been advanced as mid-level ontologies. Unfortunately, single ontologies of this sort are generally a mixture of top- and mid-level, and sometimes even of domainlevel terms. To gain clarity, we aim to specify conditions for membership in what we call the middle architecture, which consists solely of mid-level ontologies. (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)

Does the capacity to think require the capacity to sense? A lively debate on this topic runs throughout the history of philosophy and now animates discussions of artificial intelligence. Many have argued that AI systems such as large language models cannot think and understand if they lack sensory grounding. I argue that thought does not require sensory grounding: there can be pure thinkers who can think without any sensory capacities. As a result, the absence of sensory grounding does not entail (...) that large language models cannot think or understand. I also consider to what extent quasi-sensory grounding can at least boost the performance of a language model. (shrink)

In our daily lives, as in science and in all other domains, we encounter huge numbers of dispositions (tendencies, potentials, powers) which are realized in processes such as sneezing, sweating, shedding, melting. Among this plethora of what we can think of as ‘mere dispositions’ is a subset of dispositions in whose realizations we have an interest – a car responding well when driven on ice, a rabbit’s lungs responding well when it is chased by a wolf, and so on. We (...) call the latter ‘capabilities’ and we attempt to provide an ontological account of what capabilities are that is of sufficient generality to serve a variety of purposes, for example by providing a useful extension to ontology-based research in areas where capabilities data are being collected in siloed fashion. (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)

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)

What are the philosophical views of professional philosophers, and how do these views change over time? The 2020 PhilPapers Survey surveyed around 2000 philosophers on 100 philosophical questions. The results provide a snapshot of the state of some central debates in philosophy, reveal correlations and demographic effects involving philosophers' views, and reveal some changes in philosophers' views over the last decade.

A familiar interpretation of quantum mechanics (one of a number of views sometimes labeled the "Copenhagen interpretation'"), takes its empirical apparatus at face value, holding that the quantum wave function evolves by the Schrödinger equation except on certain occasions of measurement, when it collapses into a new state according to the Born rule. This interpretation is widely rejected, primarily because it faces the measurement problem: "measurement" is too imprecise for use in a fundamental physical theory. We argue that this is (...) a weak objection, as there may be many ways of making "measurement" precise. However, measurement-collapse interpretations face a more serious objection: a dilemma tied to the quantum Zeno effect. Is measurement itself an observable that can enter superpositions? If yes, then the standard measurement-collapse dynamics is ill-defined. If no, then (at least if measurement is an observable), measurements can never start or finish. The best way out is to deny that measurement is an observable, but this leads to strong and revisionary consequences. This reinforces the view that there is no nonrevisionary interpretation of quantum mechanics. (shrink)

Robbie Williams’ (2020) book The Metaphysics of Representation is the new leading edge of the program of naturalizing intentionality. Williams brings sophistica.

In this essay it is shown that the imaginative art of scientific theorizing – at its technical best – animates Quine's philosophy as importantly as the more Spartan norms honored in his present pantheon of virtues. By drawing a contrast between the standing of theories in philosophy and theories in science, it will be shown that the speculative reaches of philosophy, along with developments in semantic theory, now oblige an internal revision of Quine's stance against meaning as it was announced (...) in “Two Dogmas of Empiricism.” So, corollary to this proposed revision, I argue that in natural philosophy, the muse of the “art of science” deserves an address along with the more Spartan norms in Quine's present philosophical pantheon. As semantic theory and analyticity thus gain a measure of philosophical tenability, Quine's holism emerges as the more central doctrine of his mature vision. (shrink)

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.

Past work has shown systematic differences between Easterners' and Westerners' intuitions about the reference of proper names. Understanding when these differences emerge in development will help us understand their origins. In the present study, we investigate the referential intuitions of English- and Chinese-speaking children and adults in the U.S. and China. Using a truth-value judgment task modeled on Kripke's classic Gödel case, we find that the cross-cultural differences are already in place at age seven. Thus, these differences cannot be attributed (...) to later education or enculturation. Instead, they must stem from differences that are present in early childhood. We consider alternate theories of reference that are compatible with these findings and discuss the possibility that the cross-cultural differences reflect differences in perspective-taking strategies. (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)

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.

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)

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)

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)

David Chalmers’ two-dimensionalism is an ambitious philosophical program that aims to “ground” or “construct” Fregean meanings and restore “the golden triangle” of apriority, necessity, and meaning that Kripke seemingly broke. This paper aims to examine critically what Chalmers’ theory can in reality achieve. It is argued that the theory faces severe challenges. There are some gaps in the overall arguments, and the reasoning is in some places somewhat circular. Chalmers’ theory is effectively founded on certain strong philosophical (...) assumptions. It is concluded that it is unclear whether the theory can deliver all it promises. (shrink)

A critical notice of David J. Chalmers, Constructing the World (Oxford University Press,2012).

Chalmers (Mind 120(479): 587–636, 2011a) presents an argument against “referentialism” (and for his own view) that employs Bayesianism. He aims to make progress in a debate over the objects of belief, which seems to be at a standstill between referentialists and non-referentialists. Chalmers’ argument, in sketch, is that Bayesianism is incompatible with referentialism, and natural attempts to salvage the theory, Chalmers contends, requires giving up referentialism. Given the power and success of Bayesianism, the incompatibility is prima facie (...) evidence against referentialism. In this paper, I review Chalmers’ arguments and give some responses on behalf of the referentialist. (shrink)