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)

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)

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)

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)

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)

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)

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)

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)

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

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 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)

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)

Feminist theorists have shown that knowledge is embodied in ways that make a difference in science. Intemann properly endorses feminist standpoint theory over Longino’s empiricism, insofar as the former better addresses embodiment. I argue that a pragmatist analysis further improves standpoint theory: Pragmatism avoids the radical subjectivity that otherwise leaves us unable to account for our ability to share scientific knowledge across bodies of different kinds; and it allows us to argue for the inclusion, not just of the knowledge produced (...) from marginalised bodies, but of the marginalised themselves. (shrink)

While feminist epistemologists have made important contributions to the deconstruction of the traditional representationalist model, some elements of the Cartesian legacy remain. For example, relativism continues to play a role in the underdetermination thesis used by Longino and Keller. Both argue that because scientific theories are underdetermined by evidence, theory choice must be relative to interpretive frameworks. Utilizing Davidson's philosophy of language, I offer a nonrepresentationalist alternative to suggest how relativism can be more fully avoided.

Racist beliefs express value judgments. According to an influential view, value judgments are subjective, and not amenable to rational adjudication. In contrast, we argue that the value judgments expressed in, for example, racist beliefs, are false and objectively so. Our account combines a naturalized, philosophical account of meaning inspired by Donald Davidson, with a prominent social-psychological theory of values pioneered by the social-psychologist Milton Rokeach. We use this interdisciplinary approach to show that, just as with beliefs expressing descriptive judgments, beliefs (...) expressing value judgments have empirical content, or can be inferentially linked to beliefs that do; the truth or falsity of that content can be objectively assigned; and that assignment is amenable to rational assessment. While versions of this objective view of value judgments have been defended by moral realists of various metaphysical stripes, our argument has the virtue of appealing, instead, to accounts that are as naturalistically informed as possible. And, unlike the influential subjective view of value judgments, and racist beliefs more particularly, our arguments are better able to account for instances where rational, persuasive strategies have been effective in reducing the ubiquity of racism in American culture. (shrink)

The hygiene hypothesis offers an explanation for the correlation, well-established in the industrialized nations of North and West, between increased hygiene and sanitation, and increased rates of asthma and allergies. Recent studies have added to the scope of the hypothesis, showing a link between decreased exposure to certain bacteria and parasitic worms, and increased rates of depression and intestinal auto- immune disorders, respectively. What remains less often discussed in the research on these links is that women have higher rates than (...) men of asthma and allergies, as well as many auto-immune disorders, and also depression. The current paper introduces a feminist understanding of gender socialization to the epidemiological and immunological picture. That standards of cleanliness are generally higher for girls than boys, especially under the age of five when children are more likely to be under close adult supervision, is a robust phenomenon in industrialized nations, and some research points to a cross- cultural pattern. I conclude that, insofar as the hygiene hypothesis successfully identifies standards of hygiene and sanitation as mediators of immune health, then attention to the relevant patterns of gender socialization is important. The review also makes clear that adding a feminist analysis of gender socialization to the hygiene hypothesis helps explain variation in morbidity rates not addressed by other sources and responds to a number of outstanding puzzles in current research. Alternative explanations for the sex differences in the relevant morbidity rates are also discussed (e.g., the effects of estrogens). Finally, new sources of evidence for the hygiene hypothesis are suggested in the form of cross-cultural and other natural experiments. (shrink)

Fact/value holism has become commonplace in philosophy of science, especially in feminist literature. However, that facts are bearers of empirical content, while values are not, remains a firmly-held distinction. I support a more thorough-going holism: both facts and values can function as empirical claims, related in a seamless, semantic web. I address a counterexample from Kourany where facts and values seem importantly discontinuous, namely, the simultaneous support by the Nazis of scientifically sound cancer research and morally unsound political policies. I (...) conclude that even by the criteria available at the time, Nazi cancer research was empirically weak, and the weaknesses in their research are continuous with their moral failures in just the ways predicted by the holism I support. (shrink)

In assessing the appropriateness of a scientific community's research effort, Solomon considers a number of "decision vectors," divided into the empirical and non-empirical. Value judgments get sorted as non-empirical vectors. By way of contrast, I introduce Anderson's discussion of the evidential role of value judgments. Like Anderson, I argue that value judgments are empirical in the relevant sense. I argue further that Solomon's decision matrix needs to be reconceptualized: the distinction should not be between the empirical vs. non-empirical, but between (...) the relevant vs. irrelevant. Whether particular value judgments are relevant or not is an empirical question, to be decided on a case-by-case basis. (shrink)

: The relationship between facts and values—in particular, naturalism and normativity—poses an ongoing challenge for feminist science studies. Some have argued that the fact/value holism of W.V. Quine's naturalized epistemology holds promise. I argue that Quinean epistemology, while appropriately naturalized, might weaken the normative force of feminist claims. I then show that Quinean epistemic themes are unnecessary for feminist science studies. The empirical nature of our work provides us with all the naturalized normativity we need.

This chapter’s main topic revolves around Davidson’s account of radical interpretation and the concept of triangulation as a necessary feature of communication and the formation of beliefs. There are two important implications of this model of belief formation for feminists studying the effects of social location on knowledge production generally, and the production of scientific knowledge in particular. The first is Davidson’s argument that whatever there is to the meaning of any of our beliefs must be available from the radical (...) interpreter’s external, third-person perspective. The second important implication of triangulation is that Davidson’s model is a holistic one that shows that there is no substantive difference in the triangulation process by which we form beliefs concerning basic descriptive features of the world and beliefs concerning evaluative features of the world. (shrink)

In lieu of an abstract here is the first paragraph: -/- I mean the subtitle of my essay both as praise for the clarity with which Elizabeth Anderson writes about what is at stake in debates about values in science, and as a promise to outline an even more direct route to the heart of the matter. I begin with a quick review of the steps in Anderson’s argument that seem necessary and, indeed, laudable, followed by a brief discussion of (...) those steps in her argument that we might fruitfully skip. The hope is that we will arrive at roughly the same location but with a firmer foothold. (shrink)

The works of the later Wittgenstein resonate with aspects of the pragmatist tradition in American philosophy. Davidson’s work is similarly informed. We argue that because of their association with the pragmatist tradition, their work can be put to use by philosophers interested in social justice issues, including, for example, feminism, and critical race theory. Philosophers concerned with social justice continue to struggle between the extremes of an untenable foundationalism and a radical relativism. Given their holistic understanding of knowledge, meaning and (...) communication, the work of Wittgenstein and Davidson is particularly suited to dissolving the foundationalist/relativist dichotomy. We explore how this and other features of their work facilitates philosophy for social change. (shrink)

In 1993, biologist Margie Profet captured the attention of the popular press with the publication of her radical thesis: menstruation has a function. Traditional theories, she claims, typically view menstruation as a functionless by-product of cyclic flux. The details of Profet's functional account are similarly radical: she argues that menstruation has been naturally selected to defend the female reproductive tract from sperm-borne pathogens. There are a number of weaknesses in Profet's evolutionary analysis. However, I focus on a set of pragmatic (...) problems that arise prior to any details of her evolutionary account. In arguing for the importance of pragmatic considerations, I draw from the linguistic analyses of Nelson Goodman. I conclude that critical investigation of the evolutionary details of Profet's pathogen defense account will be more feasible if and when biologists more frequently feature the female system of pathogen defense in their inductive generalisations. The system needs to be better entrenched before its functional components, such as menstruation, can be thoroughly investigated. (shrink)

I have argued that political values are beliefs informed, more or less well, by the evidence of experience and that, where relevant and well-supported by evidence, the inclusion of political values in scientific theorizing can increase the objectivity of research. The position I endorse has been called the “values-as-evidence” approach. In this essay I respond to three kinds of resistance to this approach, using examples of feminist political values. Solomon questions whether values are beliefs that can be tested, Alcoff argues (...) that even if our values are beliefs that can be tested, testing them might not be desirable because doing so assigns these important values a contingency that weakens their normative force, and Yap argues that the approach is too idealistic in its articulation of the role of evidence in our political deliberations. In response, I discuss the ways that values can be tested, I analyze the evidential strength of feminist values in science, and I argue that the evidence-based nature of these values is neither a weakness nor an idealization. Problems with political values affecting science properly concern the dogmatic ways that evaluative beliefs are sometimes held—a problem that arises with dogmatism toward descriptive beliefs as well. I conclude that scientists, as with the rest of us, ought to adopt a pragmatically-inclined appreciation of the fallible, inductive process by which we gather evidence in support of any of our beliefs, whether they are described as evaluative or descriptive. (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.

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)

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 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)

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)

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)

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)

In Clough’s reply paper to me (http://wp.me/p1Bfg0-1aN), she laments how feminist calls for diversity within scientific communities are inadvertently sidelined by our shared feminist empiricist prescriptions. She offers a novel justification for diversity within epistemic communities and challenges me to accept this addendum to my prior prescriptions for biomedical research communities (Goldenberg 2013) on the grounds that they are consistent with the epistemic commitments that I already endorse. In this response, I evaluate and accept her challenge.

While most of healthcare research and practice fully endorses evidence-based healthcare, a minority view borrows popular themes from philosophy of science like underdetermination and value-ladenness to question the legitimacy of the evidence-based movement’s philosophical underpinnings. While the feminist origins go unacknowledged, those critics adopt a feminist reading of the “gap argument” to challenge the perceived objectivism of evidence-based practice. From there, the critics seem to despair over the “subjective elements” that values introduce to clinical reasoning, demonstrating that they do not (...) subscribe to feminist science studies’ normative program——where contextual values can enable good science and justified decisions. In this paper, I investigate why it is that the critics of evidence-based medicine adopt feminist science’s characterization of the problem but resist the productive solutions offered by those same theorists. I suggest that the common feminist empiricist appeal to idealized epistemic communities is impractical for those working within the current biomedical context and instead offer an alternate stream of feminist research into the empirical content of values (found in the work of Elizabeth Anderson and Sharyn Clough) as a more helpful recourse for facilitating the important task of legitimate and justified clinical decision-making. I use a case study on clinical decision-making to illustrate the fruitfulness of the latter feminist empiricist framework. -/- See response by Sharyn Clough: http://wp.me/p1Bfg0-1aN See reply by Maya Goldenberg: http://wp.me/p1Bfg0-1oY. (shrink)

Después de varios años bajo los efectos del boom del posmodernismo, en la década de los 90 la intelectualidad latinoamericana comenzó а recibir uп nuevo paquete de propuestas teóricas reunidas en torno al concepto “poscolonialidad”. Bajo el iпflujo de las teorías poscoloniales у los estudios subalternos se crea oficialmente en los Estados Unidos en 1994 el Grupo Latinoamericano de Estudios Subalternos (Latin American Subaltern Studies Gгoup). А el pertenecían intelectuales como Walter Mignolo, John Beverley, Alberto Moreiras, Ileana Rodríguez у (...) Norma Alarcón. Este grupo nace con la loable finalidad básica realizaг una renovación poscolonial de los llamados "Estudios de Área" norteamericanos, en particularг, de los "Latin American Studies”. En el trabajo, luego de describir algunas de las ideas más importante del grupo, se pasa a exponer, en forma de interrogantes, algunas reflexiones críticas sobre sus propuestas. (shrink)

Después de varios años bajo los efectos del boom del posmodernismo, en la década de los 90 la intelectualidad latinoamericana comenzó а recibir uп nuevo paquete de propuestas teóricas reunidas en torno al concepto “poscolonialidad”. Bajo el iпflujo de las teorías poscoloniales у los estudios subalternos se crea oficialmente en los Estados Unidos en 1994 el Grupo Latinoamericano de Estudios Subalternos (Latin American Subaltern Studies Gгoup). А el pertenecían intelectuales como Walter Mignolo, John Beverley, Alberto Moreiras, Ileana Rodríguez у (...) Norma Alarcón. Este grupo nace con la loable finalidad básica realizaг una renovación poscolonial de los llamados "Estudios de Área" norteamericanos, en particularг, de los "Latin American Studies”. En el trabajo, luego de describir algunas de las ideas más importante del grupo, se pasa a exponer, en forma de interrogantes, algunas reflexiones críticas sobre sus propuestas. (shrink)