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)

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...

Teaching ethics in public health programmes is not routine everywhere – at least not in most schools of public health in the European region. Yet empirical evidence shows that schools of public health are more and more interested in the integration of ethics in their curricula, since public health professionals often have to face difficult ethical decisions.

Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force Research Laboratory (...) (Rome) with the goal of addressing problems of these sorts through cyclical collaborative plan review and maintenance. The interactions of world state, blue force status and associated plans are too complex for manual adaptive processes, and computer-aided plan review and maintenance is thus indispensable. We argue that appropriate semantic technology can 1) provide richer representation of plan-related data and semantics, 2) allow for flexible, non-disruptive, agile, scalable, and coordinated changes in plans, and 3) support more intelligent analytical querying of plan-related data. (shrink)

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)

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)

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)

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 revisit an important exchange on the problem of radical skepticism between Richard Rorty and Michael Williams. In his contribution to this exchange, Rorty defended the kind of transcendental approach to radical skepticism that is offered by Donald Davidson, in contrast to Williams’s Wittgenstein-inspired view. It is argued that the key to evaluating this debate is to understand the particular conception of the radical skeptical problem that is offered in influential work by Barry Stroud, a conception of the (...) skeptical problem which generates metaepistemological ramifications for anti-skeptical theories. In particular, we argue that, contra Williams, Rorty’s view that Davidson was offering a theoretical diagnosis of radical skepticism can be consistently maintained with his transcendental approach. (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)

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 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)

An experimenting society is one in which policy-relevant knowledge is created. It is then critically assessed and communicated in real-life or natural settings, with the aim of discovering new forms of public action to improve the problem-solving capacities of society. This latest volume of the distinguished Policy Studies Review Annual series probes, evaluates, and augments the work of Donald T. Campbell on an experimental societies. A basic assumption of this volume is that Campbell's perspective supplies a useful way to address (...) increasingly complex and seemingly unmanageable problems facing the United States and other postindustrial societies. This volume is also the fourteenth festschrift to be issued by Transaction. The focus is on theoretical as well as practical options for creating an experimenting society. The rationale for this focus is the belief, increasingly -shared in the social science and policy-making communities alike, that researchers are essentially ignorant about how to solve many of the most pressing larger problems of this epoch. This frank recognition of ignorance is a prerequisite of genuine scientific and professional curiosity, without which knowledge gains are next to impossible to achieve, and a'precondition of an experimenting society. Contributors to this original volume include: Steve-Fuller, Duncan MacRae, Jr., Anthony S. Bryk, Robert A. Beauregard, Rita Mae Kelly, Peter Gregware, Burkart Holzner, B. Guy Peters, C. West Churchman, and Ian I. Mitroff. Their multidisciplinary competencies are at once philosophical, methodological, and substantive. They address such questions as: What new or bold policies are available in domains such as education, science, and urban development? In what ways can theoretical knowledge and practical action be fused so as to illuminate or alleviate policy problems? What should be done? Included are excerpts from Campbell's foundational paper "The Experimenting Society," as well as a recent article entitled "Methods for the Experimenting Society," which circulated in unpublished form for many years. An unusual feature of the book is Campbell's responses to those who have addressed his work with candor and intelligence. It will be of interest to policy studies scholars, sociologists, and social scientists. (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)

We present Backward Clock, an original counterexample to Robert Nozick’s truth-tracking analysis of propositional knowledge, which works differently from other putative counterexamples and avoids objections to which they are vulnerable. We then argue that four ways of analysing knowledge in terms of safety, including Duncan Pritchard’s, cannot withstand Backward Clock either.

It is argued that the arguments put forward by Bernard Williams and Thomas Nagel in their widely influential exchange on the problem of moral luck are marred by a failure to (i) present a coherent understanding of what is involved in the notion of luck, and (ii) adequately distinguish between the problem of moral luck and the analogue problem of epistemic luck, especially that version of the problem that is traditionally presented by the epistemological sceptic. It is further claimed (...) that once one offers a more developed notion of luck and disambiguates the problem of moral luck from the problem of epistemic luck (especially in its sceptical guise), neither of these papers is able to offer unambiguous grounds for thinking that there is a problem of moral luck. Indeed, it is shown that insofar as these papers succeed in making a prima facie case for the existence of epistemic luck, it is only the familiar sceptical variant of this problem that they identify. (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)

In 2006, Bill Crain was a psychology professor and his wife, Ellen, a pediatrician. They purchased a run-down farm in upstate New York, and two years later opened Safe Haven Farm Sanctuary. It is now home to over 170 animals rescued from slaughter. In Animal Stories, Bill writes about how he and Ellen decided to start the sanctuary and tells the stories of 25 animals and their many surprising behaviors. Read about Katie, a hen who cared for a little partridge; (...) Cesar, a little goat who constantly gets into trouble; Reggie, a rooster who instilled fear in all the staff; Milo, a goat who suddenly charged the dominant Duncan to defend his mother; four rambunctious young turkeys who quietly listened to a reverent Girl Scout ceremony; Ducky, a turkey who, despite severe arthritis, walked from her barn to greet a Buddhist monk; Ethel, an elderly cow who assumes the responsibility of a matriarch; and many others. In addition to enjoying the stories, readers will learn a great deal about nonhuman animals. (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.

Ronald Preston defended the middle axiom approach to doing Christian social ethics developed by J. H. Oldham for the 1937 ‘Life and Work’ conference. Preston argued that middle axioms continue to offer the churches a relevant ecumenical method. Middle axions has since been subject to fundamental criticism by ethicists such as Duncan Forrester. It will be argued that a case study of the Church of Scotland's contribution to the devolution debate, as part of Scottish civil society, supports Preston's defence (...) of the middle axiom approach as a relevant form of political engagement in the new context of local-global politics. (shrink)

Deliberative democracy is a dominant paradigm in normative political philosophy. Deliberative democrats want politics to be more than a clash of contending interests, and they believe political decisions should emerge from reasoned dialogue among citizens. But can these ideals be realized in complex and unjust societies? Deliberative Democracy in Practice brings together leading scholars who explore debates in deliberative democratic theory in four areas of practice: education, constitutions and state boundaries, indigenous-settler relations, and citizen participation and public consultation. This dynamic (...) volume casts new light on the strengths and limitations of deliberative democratic theory, offering guidance to policy makers and to students and scholars interested in democratic justice. Contributors inlcude James Bohman, Harry Brighouse, Simone Chambers, Glen Coulthard, James Fishkin, John Forester, Duncan Ivison, Micheline Milot, Henry S. Richardson, Jorge M. Valadez, and Paul Weithman. (shrink)

This paper examines the relevance of Wittgenstein’s On Certainty to the contemporary debate regarding the problem of radical scepticism. In particular, it considers two accounts in the recent literature which have seen in Wittgenstein’s remarks on “hinge propositions” in On Certainty the basis for a primarily epistemological anti-sceptical thesis—viz., the inferential contextualism offered by Michael Williams and the ‘unearned warrant’ thesis defended by Crispin Wright. Both positions are shown to be problematic, both as interpretations of Wittgenstein and as anti-sceptical (...) theses. Indeed, it is argued that on a reading of On Certainty which has Wittgenstein advancing a primarily epistemological thesis, there is in fact strong evidence to suggest that Wittgenstein thought that no epistemic response to the sceptic was available—at best, it seems, only a pragmatic antisceptical thesis is on offer. Such a conclusion is not without import to the present debate regarding radical scepticism, however, since it poses a general challenge for how the sceptical argument is conceived in the contemporary literature. (shrink)

This chapter contains sections titled: Abstract From the Epistemology of Disagreement to Epistemic Relativism The Irrelevance of Epistemic Externalism Wittgensteinian Epistemology and Epistemic Relativism Williams's Wittgensteinian Contextualism Wittgensteinian Epistemology Reconsidered Concluding Remarks References.

The recent popularity of contextualist treatments of the key epistemic concepts has tended to obscure the differences that exist between the various kinds of contextualist theses on offer. The aim of this paper is to contribute towards rectifying this problem by exploring two of the main formulations of the contextualist position currently on offer in the literature—the 'semantic' contextualist thesis put forward by Keith DeRose and David Lewis, and the 'inferential' contextualist thesis advanced by Michael Williams. It is argued (...) that by evaluating these theses in the light of each other one can gain a deeper understanding of the contextualist position. In particular, it is argued that this relative evaluation highlights one interesting way in which contextualism might be developed. (shrink)

This chapter looks at the discussion of materialism in John Locke’s Essay concerning Human Understanding, and then at parts of the Anglophone reaction to those discussions. It considers the early criticisms of Locke by Edward Stillingfleet and the anonymous author of three sets of Remarks on Locke’s Essay. It then looks at some other ways in which readers reacted to Locke’s discussions: the views of Anthony Collins and John Toland, which one might be tempted to think of as Lockean materialism; (...) William Carroll’s reading of Locke as a Spinozistic materialist; and the dualistic Lockeanism of William Duncan’s Lockean logic textbook. (shrink)

It is maintained that the arguments put forward by Bernard Williams and Thomas Nagel in their widely influential exchange on the problem of moral luck are marred by a failure to (i) present a coherent understanding of what is involved in the notion of luck, and (ii) adequately distinguish between the problem of moral luck and the analogue problem of epistemic luck, especially that version of the problem that is traditionally presented by the epistemological sceptic. It is further claimed (...) that once one offers a more developed notion of luck and disambiguates the problem of moral luck from the problem of epistemic luck (especially in its sceptical guise), neither of these papers is able to offer unambiguous grounds for thinking that there is a problem of moral luck. Indeed, it is shown that in so far as these papers succeed in making a prima facie case for the existence of epistemic luck, it is only the familiar sceptical variant of this problem that they identify. (shrink)