There are a wide range of positions regarding the ontological nature of computer hardware and software. Moor [The British Journal for the Philosophy of Science 29 (1978), 213–222] argues that there...

The 10th International Conference on Biomedical Ontology (ICBO 2019), was held at the Jacobs School of Medicine and Biomedical Sciences of the University at Buffalo, in Buffalo, NY, USA. It was the 10-year anniversary of the ICBO series, and the return of the conference to Buffalo after the first two ICBO conferences were held in Buffalo in 2009 and 2011. ICBO 2019 was well attended, with 115 registered attendees and additional walk-ins from the local academic community. The program included excellent (...) keynote talks by Barry Smith, “International Standard Ontology,” and Bjoern Peters, “Putting principles into practice: OBO ontologies and applications in immunology,” as well as 23 oral presentations, 26 posters, and one software presentation. There were 53 papers and abstracts submitted for peer-review to ICBO 2019. Each submission was reviewed by three members chosen from the Program Committee. Of these submissions, 43 were accepted for this volume: 19 full papers, 23 poster abstracts, and 1 software demonstration extended abstract. We thank our program committee for their thoughtful reviews. There were also three workshops and four tutorials (listed below) held in conjunction with the main ICBO 2019 meeting. (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)

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (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)

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)

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)

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)

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)

This volume contains thirteen papers that were presented at the 2017 Annual Meeting of the Canadian Society for History and Philosophy of Mathematics/Société canadienne d’histoire et de philosophie des mathématiques, which was held at Ryerson University in Toronto. It showcases rigorously reviewed modern scholarship on an interesting variety of topics in the history and philosophy of mathematics from Ancient Greece to the twentieth century. A series of chapters all set in the eighteenth century consider topics such as John Marsh’s techniques (...) for the computation of decimal fractions, Euler’s efforts to compute the surface area of scalene cones, a little-known work by John Playfair on the practical aspects of mathematics, and Monge’s use of descriptive geometry. After a brief stop in the nineteenth century to consider the culture of research mathematics in 1860s Prussia, the book moves into the twentieth century with an examination of the historical context within which the Axiom of Choice was developed and a paper discussing Anatoly Vlasov’s adaptation of the Boltzmann equation to ionized gases. The remaining chapters deal with the philosophy of twentieth-century mathematics through topics such as an historically informed discussion of finitism and its limits; a reexamination of Mary Leng’s defenses of mathematical fictionalism through an alternative, anti-realist approach to mathematics; and a look at the reasons that mathematicians select specific problems to pursue. Written by leading scholars in the field, these papers are accessible to not only mathematicians and students of the history and philosophy of mathematics, but also anyone with a general interest in mathematics. (shrink)

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)

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.

An analytical investigation into compressible gas flow with slight rarefactions through the insect trachea and tracheoles during the closed spiracle phase is undertaken, and a complete set of asymptotic analytical solutions is presented. We first obtain estimates of the Reynolds and Mach numbers at the channel terminal ends where the tracheoles directly deliver respiratory gases to the cells, by comparing the magnitude of the different forces in the compressible gas flow. The 2D Navier–Stokes equations with a slip boundary condition are (...) used to investigate compressibility and rarefied effects in the trachea and tracheoles. Expressions for the velocity components, pressure gradients and net flow inside the trachea are then presented. Numerical simulations of the tracheal compressible flow are performed to validate the analytical results from this study. This work extends previous work of Arkilic et al. :167–178, 1997) on compressible flows through a microchannel. Novel devices for microfluidic compressible flow transport may be invented from results obtained in this study. (shrink)

David Hume’s ‘History of England’ is an ambitious work that helps demonstrate how the modern historian can interpret the crucial events that define human communities as continuous in time. This paper is directly concerned with the significance of Hume's historical method, his view of human agency and the role of the English Constitution in appraising the meaning of secularity in his historical work. The more fundamental purpose of the paper will be to show that the study of history was not (...) incidental to his task as a philosopher but, on the contrary, relates to his deeper view of how we experience the world in terms of fundamental categories of time and meaning. (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 (écriture). 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)

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)

Discriminating behavior depends on neural representations in which the sensory activity patterns guiding different responses are decorrelated from one another. Visual information can often be parsimoniously transformed into these behavioral bridge-locus representations within neuro-computational visuo-spatial maps. Isomorphic inverse-optical world representation is not the goal. Nevertheless, such useful transformations can involve neural filling-in. Such a subpersonal representation of information is consistent with personal-level vision theory.

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)

Some scholars have speculated whether the conservative New Testament Calvinistic scholar, Machen and the New Testament critical scholar, Bultmann attended Marburg University at the same time. We now know that they did. They even attended two courses together which were taught respectively by Weiss and Jülicher. Although these men were strong opposites with respect to the environment in which they were raised as well as their theological presuppositions and conclusions, they both enjoyed the engaging environment of Marburg as students. Mainly (...) using personal letters, we learn that a comparison of these two young students goes further than their theological and biblical interests. Both had encyclopedic academic interests which carried over into a fascinating interdisciplinary way of life. (shrink)

Thomas Hobbes often includes powers and abilities in his descriptions of the world. Meanwhile, Hobbes’s philosophical picture of the world appears quite reductive, and he seems sometimes to say that nothing exists but bodies in motion. In more extreme versions of such a picture, there would be no room for powers. Hobbes is not an eliminativist about powers, but his view does tend toward ontological minimalism. It would be good to have an account of what Hobbes thinks powers are, and (...) how they fit into his understanding of the world. In this chapter, I investigate Hobbes’s account of the metaphysics of powers and abilities. Section 1 considers three important aspects of Hobbes’s account of powers: the connection between powers and causes; the modal aspects of powers; and the connection between powers and motions. Sections 2 and 3 then consider interpretive arguments about whether Hobbes identifies powers with underlying corporeal features. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:“Analyzing How Rhetoric is Epistemic”:A Reply to Steve FullerWilliam D. HarpineMy point in "What Do You Mean, Rhetoric Is Epistemic" (Harpine 2004) is that unclear and inconsistent use of terms has hindered previous research on the idea that rhetoric is epistemic. I propose to clarify definitions to alleviate this problem and encourage further research into how rhetoric might be epistemic. Professor Fuller's viewpoint is that definitions are inherently problematic, (...) and that my call for rhetoric-is-epistemic theorists to formulate their definitions more carefully would hold rhetorical theory to "illusory" standards (Fuller 2005, 72). However, I feel that his criticism of definitions overstates what his arguments demonstrate. Fuller (2005) also expresses doubts about the concept of certainty, doubts which echo points in my essay. Along the way, he offers an interesting line of reasoning that might advance the dialogue in the way that I had hoped. To an extent, Fuller seems to reach similar conclusions about the relationship between rhetoric and knowledge, albeit by a different route.CertaintyMy essay argues that certain claims of rhetoric-is-epistemic theorists trade on an equivocation about the meaning of "certainty." The word "certain" can carry an objective meaning: "It is certain that I will have to pay taxes," or it can be subjective: "I feel certain that I will have to pay taxes." An ordinary person can easily see that the two claims mean something different. Although Wittgenstein explains this distinction most clearly, in a statement that Fuller (2005) himself quotes, the distinction routinely arises in everyday discourse. An argument that works surreptitiously by sliding from one of these meanings to the other commits the fallacy of equivocation. The rhetoric-is-epistemic literature does exactly that all too often. [End Page 82]On this matter, expressing doubts about objective certainty, Fuller comments that the role of certainty in philosophy is inconclusive (2005, 78). I fully agree with this point. My argument is to show how rhetoric-is-epistemic theorists fallaciously rely on an ambiguity in meaning, not to claim that some things really are objectively certain. It is not the purpose of rhetoric-is-epistemic theorists to argue that nothing is certain—there are much more straightforward ways to do that—but to show that rhetoric has an epistemic role. To accomplish this, they need an argument that does not short-circuit by equivocating in the use of key terms. In any case, my essay notes that "the current philosophical literature has not taken a strong stance in favor of requiring knowledge to be either objectively or subjectively certain," which resembles Fuller's own conclusion, and also that rhetoric-is-epistemic theorists "should dispense with the issue of certainty" (Harpine 2004, 346), which, if Fuller agrees (as I suspect he does), renders further details moot.KnowledgeMost rhetoric-is-epistemic theorists work either explicitly or implicitly with the traditional definition that knowledge is justified true belief. They point out that rhetoric offers justification. Gettier's argument shows that the traditional definition fails to capture the meaning of "knowledge." Thus, the rhetoric-is-epistemic theorists have a problem tying their theory to their conception of knowledge. The point is not that different rhetoric-is-epistemic theorists have used different definitions of knowledge, but rather that they work with an inadequate definition. Fuller agrees with Gettier's point, gives additional arguments on its behalf, and offers an interesting discussion of the rhetorical implications of Gettier's argument. Since Gettier's argument may lead one to question whether justification is a defining quality of knowledge, rhetoric-is-epistemic theorists might look for other kinds of linkages between rhetoric and knowledge. The concluding portions of my essay suggest several such possible linkages.1Does my argument resemble the Babel thesis? Elsewhere, Fuller (2002, 104) explains the Babel thesis as the claim that disagreements are due to different meanings, not to different beliefs. One must agree with Fuller that the Babel thesis overstates the importance of meaning. However, a similar insight arises in more modest guise as Davidson's principle [End Page 83] of charity. Studying intercultural relationships, Davidson (1984, 136) suggests that when we encounter people whose beliefs differ from ours, we... (shrink)

The purpose of this paper is to demonstrate that the novels of Jean Rhys embody a significant use of myths, which can be interpreted in terms of the postcolonial as a historical category. The paper does not argue that Rhys was invariably a postcolonial writer but that the postcolonial as a category casts light on her work as a novelist. In addition to employing semiotics and postcolonial theory, this paper also enlists Homi Bhabha's appropriation of Lacan as a tool in (...) reading. The postcolonial text that gradually emerges in Rhys's novels is shown to inform the various "semiotic mythologies" that dominate her work as a whole. (shrink)

Intradermal capsaicin in humans causes pain, primary hyperalgesia, and secondary mechanical hyperalgesia and allodynia. Parallel changes occur in the responses of primate spinothalamic tract cells and in rat behavior. Neurotransmitters that trigger secondary mechanical hyperalgesia and allodynia include excitatory amino acids and substance P. Secondary mechanical allodynia is actively maintained by central mechanisms. Our group has investigated mechanisms of central sensitization of nociceptive neurons by examining the responses to intradermal injection of capsaicin. These experiments are pertinent to issues raised by (...) coderre & katz (sect. 2). (shrink)

The development of comparative biology has been of interest to philosophers and historians. Particular attention has been placed on the ‘war’ of the 1970s and 1980s, the apparent dispute among those who preferred this or that methodology. In this contribution we examine the history of comparative biology from the perspective of fundamentals rather than methodologies. Our examination is framed within the artificial—natural classification dichotomy, a viewpoint currently lost from view but worth resurrecting.

This collection of essays is concerned with Paul de Man's work as a literary theorist, particularly his later, linguistically-informed contribution to the reading and interpretation of literature. The essays in this collection argue that de Man's legacy is complex and multidimensional. Paul de Man's work in "deconstructive" literary criticism is examined in some detail with regard to its continuing pertinence to recent developments in literary study. This collection argues persuasively that de Man's work continues to be important to the so-called (...) "afterlife" of theory. (shrink)

Volume 24, Issue 7-8, November - December 2019, Page 871-872.