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)

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)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

This anthology is the first devoted exclusively to On Certainty. The essays are grouped under four headings: the Framework, Transcendental, Epistemic and Therapeutic readings, and an introduction helps explain why these readings need not be seen as antagonistic. Contributions from W.H. Brenner, Alice Crary, Michael Kober, Edward Minar, Howard Mounce, Daniele Moyal-Sharrock, Thomas Morawetz, D.Z. Phillips, Duncan Pritchard, Rupert Read, Anthony Rudd, Joachim Schulte, Avrum Stroll, Michael Williams.

Experiential acquaintance is an alleged relation between ourselves and our experiences that has sometimes been hypothesised as necessary for knowledge of our experiences. This paper begins with a clarification of ‘acquaintance’ and an explanation of ‘experience’ that focuses attention on a famous, but flawed, argument by G. E. Moore. It goes on to critically examine several recent arguments concerning experiential acquaintance and to show how internalist foundationalism can respond to a famous Sellarsian dilemma without appeal to a relation of acquaintance (...) with our experiences. It concludes that we can dispense with experiential acquaintance. (shrink)

To date, there have been only two scholarly papers devoted to a comparison of Gestalt psychology with the psychology of William James. An early paper by Mary Whiton Calkins called attention to numerous similarities between these two schools of thought. However, a more recent paper by Mary Henle argues that the ideas of William James, as presented in The Principles of Psychology, are irrelevant to Gestalt psychology. In what follows, this claim is evaluated both in terms of The (...) Principles and Jamesís larger vision as set forth in his mature philosophical works. Although there are important differences between James and the Gestalt psychologists, there are also striking similarities particularly when the two schools are examined in the light of Jamesís mature philosophical perspectives. (shrink)

In Natural Ethical Facts William Casebeer argues that we can articulate a fully naturalized ethical theory using concepts from evolutionary biology and cognitive science, and that we can study moral cognition just as we study other forms of cognition. His goal is to show that we have "softly fixed" human natures, that these natures are evolved, and that our lives go well or badly depending on how we satisfy the functional demands of these natures. Natural Ethical Facts is a (...) comprehensive examination of what a plausible moral science would look like.Casebeer begins by discussing the nature of ethics and the possible relationship between science and ethics. He then addresses David Hume's naturalistic fallacy and G. E. Moore's open-question argument, drawing on the work of John Dewey and W. V. O. Quine. He then proposes a functional account of ethics, offering corresponding biological and moral descriptions. Discussing in detail the neural correlates of moral cognition, he argues that neural networks can be used to model ethical function. He then discusses the impact his views of moral epistemology and ontology will have on traditional ethical theory and moral education, concluding that there is room for other moral theories as long as they take into consideration the functional aspect of ethics; the pragmatic neo-Aristotelian virtue theory he proposes thus serves as a moral "big tent." Finally, he addresses objections to ethical naturalism that may arise, and calls for a reconciliation of the sciences and the humanities. "Living well," Casebeer writes, "depends upon reweaving our ethical theories into the warp and woof of our scientific heritage, attending to the myriad consequences such a project will have for the way we live our lives and the manner in which we structure our collective moral institutions.". (shrink)

This book is a systematic reconstruction of Heidegger's account of time and temporality in Being and Time. The author locates Heidegger in a tradition of 'temporal idealism' with its sources in Plotinus, Leibniz, and Kant. For Heidegger, time can only be explained in terms of 'originary temporality', a concept integral to his ontology. Blattner sets out not only the foundations of Heidegger's ontology, but also his phenomenology of the experience of time. Focusing on a neglected but central aspect of Being (...) and Time, this book will be of considerable interest to all students of Heidegger both inside and outside philosophy. (shrink)

In Natural Ethical Facts William Casebeer argues that we can articulate a fully naturalized ethical theory using concepts from evolutionary biology and cognitive science, and that we can study moral cognition just as we study other forms of cognition. His goal is to show that we have "softly fixed" human natures, that these natures are evolved, and that our lives go well or badly depending on how we satisfy the functional demands of these natures. Natural Ethical Facts is a (...) comprehensive examination of what a plausible moral science would look like.Casebeer begins by discussing the nature of ethics and the possible relationship between science and ethics. He then addresses David Hume's naturalistic fallacy and G. E. Moore's open-question argument, drawing on the work of John Dewey and W. V. O. Quine. He then proposes a functional account of ethics, offering corresponding biological and moral descriptions. Discussing in detail the neural correlates of moral cognition, he argues that neural networks can be used to model ethical function. He then discusses the impact his views of moral epistemology and ontology will have on traditional ethical theory and moral education, concluding that there is room for other moral theories as long as they take into consideration the functional aspect of ethics; the pragmatic neo-Aristotelian virtue theory he proposes thus serves as a moral "big tent." Finally, he addresses objections to ethical naturalism that may arise, and calls for a reconciliation of the sciences and the humanities. "Living well," Casebeer writes, "depends upon reweaving our ethical theories into the warp and woof of our scientific heritage, attending to the myriad consequences such a project will have for the way we live our lives and the manner in which we structure our collective moral institutions.". (shrink)

The purpose of this article should become plain during the reading of it, but perhaps some prior explanation is needed. Almost from the beginning of my study of the paṭiccasamuppāda I have had the notion that it could not have come into existence in the form the usual twelvefold formulation takes. For reasons which I try to make clear this twelvefold formulation is not a satisfactory statement of what it is supposed to explain, namely the reasons for each individual's continued (...) rebirths. I feel - and sadly I have to emphasize, before someone else does it for me, that in the final analysis I am relying more or less on intuition for my attitude towards the twelvefold formulation - that if one person alone had been responsible for the usually referred to formulation, and especially if that one person had been the Buddha, then those anomalies that now prevail would never have existed. (shrink)

Schanbacer, William D: The Politics of Food: The Global Conflict Between Food Security and Food Sovereignty Content Type Journal Article DOI 10.1007/s10806-010-9267-1 Authors Cornelia Butler Flora, Iowa State University 317 East Hall Ames IA 50011-1070 USA Journal Journal of Agricultural and Environmental Ethics Online ISSN 1573-322X Print ISSN 1187-7863.

The purpose of this paper is to examine the central role of praxis in Arendt’s conception of the human world and the structure of political life as a site of subjective interaction and narrative discourse. First, Arendt’s use of Aristotle will be presented in terms of the meaning of action as a unique philosophical category. Second, Arendt’s encounter with the work of Martin Heidegger will be shown to involve a critical response to his reading of Aristotle. Finally, the revised conception (...) of praxis that derives from her philosophical reflections will be related to the experience of narrative as a necessary complement to human plurality. (shrink)

Adorno’s dialectical approach to aesthetics is perhaps understood better in terms of his monumental work, 'Aesthetic Theory,' which attempts to relate the speculative tradition in philosophical aesthetics to the situation of art in twentieth-century society, than in terms of purely theoretical claims. This paper demonstrates that Adorno embraces the Kantian thesis concerning art’s autonomy and that he criticizes transcendental philosophy. It also discusses how Adorno provides the outlines for a dialectical conception of artistic truth in relation to his argument with (...) Hegel. Adorno’s assessment of the Enlightenment is linked to his interpretation of twentieth-century literature. The conclusion of this paper emphasizes the political implications of Adorno’s position when the philosopher approaches art as a sign of historical truth. (shrink)

A central theme to be found in Dewey’s writings is his criticism of theories of knowledge proposed throughout the history of Western philosophy. None of the once familiar “isms,” whether it be a variant of empiricism, rationalism, or idealism, escaped Dewey’s scrutiny. And each in its turn proved to be unacceptable to Dewey, because it was found that each rested upon what Dewey referred to as “the philosophical fallacy,” namely “the conversion of eventual functions into antecedent existence,” or the fallacy (...) of selective emphasis. Basically, this fallacy amounted for Dewey to the emphasis of one aspect of scientific inquiry to the exclusion of the rest, and taking the features characteristic of that aspect as paradigmatic for the purpose of accounting for knowledge. Thus, for example, advocates of what Dewey called sensationalism, for whom knowledge was to be explicated in terms of an immediate acquaintance with a perceptual given, emphasized an aspect of scientific inquiry, viz., that inquiry is engaged in only when some given situation is problematic, without regard to the fact that even those features of a problematic situation, which are taken to be given and stable features for purposes of resolving the problem, are so taken only provisionally, depending upon whether the ensuing inquiry is successful in resolving the problem at hand. (shrink)

As presented in the early work, 'Revolution in Poetic Language,' Julia Kristeva’s 'subject-in-process' can be interpreted as a semiotic alternative to older conceptions of the philosophical subject.This discussion of Kristeva’s early work will attempt to demonstrate that new interpretations of Fregean logic and Freudian psychoanalysis radically displace the traditional subject. This act of displacement allows Kristeva to employ Hegelian dialectics to introduce a “textual” conception of meaning of experience. As a consequence, the Kristevan semiotexte offers a basis for both understanding (...) and misunderstanding in which language mediates between semiotic meaning and cultural practices. The conclusion of the paper maintains that Kristeva's unique formulation of the semiotexte re-defines human subjectivity in relation to the existing world. (shrink)

Ikujiro Nonaka, whose formative experience is Japanese, is an established scholar who has written about large business organizations. He sees knowledge at the heart of the organization and its products and aims to develop Michael Polanyi’s conception of tacit knowledge in a practical direction to enhance organizational “knowledge creation.” For Nonaka, what matters is the practice, the doing, the embodiment of knowledge. An organization can amplify and crystallize individuals’ tacit knowledge in a process that allows them to experience deeper understanding. (...) Nonaka holds that it is iimportant to explore the potential that knowledge holds. His spiral process describes disciplined practices that make tacit knowledge independent and available to restructure the organizational knowledge context. (shrink)

The present paper defends the thesis that Spenser's recovery of place, as enacted in 'The Faerie Queene,' Book VI, can be linked in a direct way to his use of a poetic phenomenology which informs and clarifies his work as an epic writer. Spenser's "Book of Courtesy" enacts a Neo-Platonic movement from the lower levels of temporal existence to an exalted vision of spiritual perfection. The paper explores this movement along phenomenological lines as a mysterious adventure that embraces self and (...) other, personality and community, aesthetics and ethics, in a sequence of images that opens up a new interpretation of imaginative fulfillment. (shrink)

This paper argues that Hegel attempts to appropriate the irreversible aspects of Romantic aesthetics in four ways: (i) Hegel radicalizes Kantian aesthetics on the basis of a basically textual approach to sublime experience that opens up the question of community as a philosophical one; (ii) without demoting classical conceptions of art, Hegel privileges Romantic conceptions that demonstrate the ascendancy of sign over symbol in a spiraling chain; (iii) Hegel laments the fate of art in the triumph of Romantic subjectivism but (...) also suggests how communities can reconstitute themselves on the horizon of aesthetic dissolution; so that, finally, (iv) art can be reconceived as a emancipatory adventure that redefines metaphysics through its historical unfolding as an unending series of semiotic transformations. (shrink)

This paper argues that Paul Ricoeur’s hermeneutical philosophy attempts to reopen the question of human transcendence in contemporary terms. While his conception of language as self-transcending is deeply Husserlian, Ricoeur also responds to the analytical challenge when he deploys a basic distinction in Fregean logic in order to clarify Heidegger’s phenomenology of world. Ricoeur’s commitment to a transcendental view is evident in his conception of narrative, which enables him to emphasize the role of the performative in literary reading. The meaning (...) of the self in time provides Ricoeur with a discursive basis for distinguishing his own position from that of Kant and other philosophers in the transcendental tradition. (shrink)

Heidegger's interpretation of Nietzsche has been canonized in the philosophical tradition as an almost perfect demonstration of how the forgetfulness of Being continues the dominant positions of modern metaphysics. However, the role of reading in the interpretative process casts a different light on Heidegger's approach to Nietzsche and his relationship to the philosophical tradition. This paper is concerned with three aspects of Heidegger's work, namely, (i) the role of Kant and Schopenhauer in Nietzsche's critique of metaphysics; (ii) Nietzsche's 'inversion' of (...) Platonism; and (iii) Heidegger's contribution to a hermeneutical reappraisal of Nietzsche's thought. (shrink)

The last 100 years can be described as pivotal in our appreciation of human rights. From the Déclaration des droits internationaux de l'homme of 1929 to the more recent discussion of the establishment of an International Court of Justice, the notions of 'rights' and 'international human rights' have extended beyond rarefied philosophical discourse to become part of our basic vocabulary. The United Nations Universal Declaration of Human Rights (UDHR) of 1948 is a key document that is central to contemporary dialogues (...) about human rights. The UDHR and its subsequent protocols and conventions enumerate a lengthy list of rights that many recognize as fundamental in ensuring human dignity. Philosophical Theory and the Universal Declaration of Human Rights examines the relations and interrelations among theoretical and practical analyses of human rights. Edited by William Sweet, this extensive volume draws on the work of philosophers, political theorists, and those involved in the implementation of human rights. Although diverse in subject and approach, the essays collectively argue that the language of rights and the corresponding legal and political instruments have an important place in contemporary social and political philosophy. (shrink)

The logical connection argument holds that factors which appear causally connected can be shown not to be so, At least when described in certain ways, If these factors are logically connected when so described. I argue that normal formulations of the logical connection argument confuse propositions and events. Moreover, When it is clarified in terms of "de re" necessity, It requires strong ontological assumptions for which no support is given and about the intelligibility of which there is reasonable question. I (...) conclude that the logical connection argument fails to give any reason for excluding any causal hypothesis. (shrink)

This paper is concerned with Maurice Merleau-Ponty’s contribution to the hermeneutical theory of expressive meaning that has been developed on the basis of an ongoing dialogue with traditional phenomenology. The early portion of the paper examines the unstable boundaries between expression and indication as a key to a new approach to expressive meaning. The paper then takes up Merleau-Ponty’s understanding of expressive life as it emerges in ‘Phenomenology of Perception,’ his first attempt to discuss perception, aesthetics, and temporality in comprehensive (...) terms. The third part of the paper examines Merleau-Ponty’s return to the paintings of Paul Cezanne, which not only clarifies his earlier position but also deepens the philosophical meaning of his reflections on language. My final comments are concerned with how phenomenology can be broadened in a way that can become responsive to the hermeneutical theory of expressive meaning. (shrink)

The paper argues that Sartre’s work as both a literary critic and social philosopher is deeply indebted to his early commitment to phenomenology. The first part of the paper examines the nature of reading and writing in the account of literary meaning that is presented in the transitional text, 'Qu’est-ce que la littérature?' While acknowledging the political turn that occurs in Sartre’s work, we then discuss how the theme of history emerges in the later essay, 'Questions de méthode,' as one (...) that opens up a “double reading” of human motivation. Our conclusion maintains that the Marxist phase of Sartre’s work is based on the hermeneutical notion of comprehension, which provides an anthropological grounding for his existential philosophy. (shrink)

We critically review themushrooming literature addressing the neuralmechanisms of moral cognition (NMMC), reachingthe following broad conclusions: (1) researchmainly focuses on three inter-relatedcategories: the moral emotions, moral socialcognition, and abstract moral reasoning. (2)Research varies in terms of whether it deploysecologically valid or experimentallysimplified conceptions of moral cognition. Themore ecologically valid the experimentalregime, the broader the brain areas involved.(3) Much of the research depends on simplifyingassumptions about the domain of moral reasoningthat are motivated by the need to makeexperimental progress. This is a (...) valuablebeginning, but as more is understood about theneural mechanisms of decision-making, morerealistic conceptions will need to replace thesimplified conceptions. (4) The neuralcorrelates of real-life moral cognition areunlikely to consist in anything remotely like a``moral module'' or a ``morality center.'' Moralrepresentations, deliberations and decisionsare probably highly distributed and notconfined to any particular brainsub-system. Discovering the basic neuralprinciples governing planning, judgment anddecision-making will require vastly more basicresearch in neuroscience, but correlatingactivity in certain brain regions withwell-defined psychological conditions helpsguide neural level research. Progress on socialphenomena will also require theoreticalinnovation in understanding the brain'sdistinctly biological form of computationthat is anchored by emotions, needs, drives,and the instinct for survival. (shrink)

The main purpose of this paper is to demonstrate how Gianni Vattimo offers a new interpretation of history that challenges standard accounts of the modern period and promotes a new approach to literature. The paper begins with a discussion of how the Cartesian cogito provides an inadequate basis for historical research, and then proposes that modern history can be 'read' when it is reassessed through recent hermeneutics. In 'The End of Modernity' (1985), Vattimo indicates that Heidegger's understanding of the "overcoming (...) of metaphysics" shifted in time, thus suggesting new insights into modernity. The conclusion to the paper applies these insights to show how the notion of a unified literary period is difficult to sustain in a postmodern framework. -/- . (shrink)

This book is concerned with the continuing viability of both Freud and Hegel to the reading of modern literature. The book begins with Julia Kristeva’s attempts to relate Hegelian thought to a psychoanalytically informed conception of semiotics that was first explored in her influential study, The Revolution of Poetic Language, and then modified in later books that develop semiotics in new directions. Kristeva’s agreements and disagreement with Hegel are important to the book’s argument, which ultimately defends Hegel against familiar, poststructuralist (...) detractions. However, the book’s conceptual argument requires a historical exposition, with chapters devoted to literary figures ranging from Spenser to Ishiguro. One of the purposes of the book is to demonstrate that Hegel’s contribution to modern thought is at least partially exhibited in the history of literature, which also corroborates some of the deeper insights of psychoanalysis. (shrink)

Material Difference: Modernism and the Allegories of Discourse argues that deconstruction can be employed in conjunction with the historically-oriented approach to cultural experience that is favored by Critical Theory. The two discourses that inform this comparative study situate Modernism between evolving traditions that begin with Hegel and Nietzsche, leading on to Adorno’s commitment to philosophical aesthetics and Derrida’s concern for writing . Interrelated discussions of eight major authors, working in four different languages, are presented to show how allegorical Modernism foreshadows (...) the possibility of cultural history. Joyce, Kafka, Malraux, Rilke, and Stevens are among the authors discussed in this book. The notion of material difference allows literature to be redefined in semiotic terms and demonstrates how the allegorical imagination mediates between art and time. (shrink)

Dr Hart sets out to answer this question by showing that the issue is as much about the nature of causation as it is about the natures of mind and matter.