Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

This book is a survey of the most important developments in Austrian philosophy in its classical period from the 1870s to the Anschluss in 1938. Thus it is intended as a contribution to the history of philosophy. But I hope that it will be seen also as a contribution to philosophy in its own right as an attempt to philosophize in the spirit of those, above all Roderick Chisholm, Rudolf Haller, Kevin Mulligan and Peter Simons, who have done so much (...) to demonstrate the continued fertility of the ideas and methods of the Austrian philosophers in our own day. For some time now, historians of philosophy have been gradually coming to terms with the idea that post-Kantian philosophy in the German-speaking world ought properly to be divided into two distinct traditions which we might refer to as the German and Austrian traditions, respectively. The main line of the first consists in a list of personages beginning with Kant, Fichte, Hegel and Schelling and ending with Heidegger, Adorno and Bloch. The main line of the second may be picked out similarly by means of a list beginning with Bolzano, Mach and Meinong, and ending with Wittgenstein, Neurath and Popper. As should be clear, it is the Austrian tradition that has contributed most to the contemporary mainstream of philosophical thinking in the Anglo-Saxon world. For while there are of course German thinkers who have made crucial contributions to the development of exact or analytic philosophy, such thinkers were outsiders when seen from the perspective of native German philosophical culture, and in fact a number of them found their philosophical home precisely in Vienna. When, in contrast, we examine the influence of the Austrian line, we encounter a whole series of familiar and unfamiliar links to the characteristic concerns of more recent philosophy of the analytic sort. As Michael Dummett points out in his Origins of Analytic Philosophy, the newly fashionable habit of referring to analytic philosophy as "Anglo-American" is in this light a "grave historical distortion". If, he says, we take into account the historical context in which analytic philosophy developed, then such philosophy "could at least as well be called "Anglo-Austrian" (1988, p. 7). Much valuable scholarly work has been done on the thinking of Husserl and Wittgenstein, Mach and the Vienna Circle. The central axis of Austrian philosophy, however, which as I hope to show in what follows is constituted by the work of Brentano and his school, is still rather poorly understood. Work on Meinong or Twardowski by contemporary philosophers still standardly rests upon simplified and often confused renderings of a few favoured theses taken out of context. Little attention is paid to original sources, and little effort is devoted to establishing what the problems were by which the Austrian philosophers in general were exercised -- in spite of the fact that many of these same problems have once more become important as a result of the contemporary burgeoning of interest on the part of philosophers in problems in the field of cognitive science. (shrink)

Analytic philosophers have until recently been reluctant to pursue historical investigations into the Central European roots of their own philosophical tradition. The most recent book by Michael Dummett, however, entitled Origins of Analytic Philosophy, shows how fruitful such investigations can be, not only as a means of coming to see familiar philosophical problems in a new light, but also as a means of clarifying what, precisely, ‘analytic philosophy’ might mean. As Dummett points out, the newly fashionable habit of referring (...) to analytic philosophy as ‘Anglo-American’ leads to a ‘grave historical distortion’. If, he says, we take into account the historical context in which analytic philosophy developed, then such philosophy ‘could at least as well be called "Anglo-Austrian"’ (p. 7). We here show the implications of this assertion for a more adequate understanding of the relations between analytic and Continental philosophy. (shrink)

Analytic philosophers have until recently been reluctant to pursue historical investigations into the Central European roots of their own philosophical tradition. The most recent book by Michael Dummett, however, entitled Origins of Analytic Philosophy, shows how fruitful such investigations can be, not only as a means of coming to see familiar philosophical problems in a new light, but also as a means of clarifying what, precisely, ‘analytic philosophy’ might mean. As Dummett points out, the newly fashionable habit of referring (...) to analytic philosophy as ‘Anglo-American’ leads to a ‘grave historical distortion’. If, he says, we take into account the historical context in which analytic philosophy developed, then such philosophy ‘could at least as well be called "Anglo-Austrian"’ (p. 7). We here show the implications of this assertion for a more adequate understanding of the relations between analytic and Continental philosophy. (shrink)

In May 2010, philosophers, family and friends gathered at the University of Notre Dame to celebrate the career and retirement of Alvin Plantinga, widely recognized as one of the world's leading figures in metaphysics, epistemology, and the philosophy of religion. Plantinga has earned particular respect within the community of Christian philosophers for the pivotal role that he played in the recent renewal and development of philosophy of religion and philosophical theology. Each of the essays in this volume engages with some (...) particular aspect of Plantinga's views on metaphysics, epistemology, or philosophy of religion. Contributors include Michael Bergman, Ernest Sosa, Trenton Merricks, Richard Otte, Peter VanInwagen, Thomas P. Flint, Eleonore Stump, Dean Zimmerman and Nicholas Wolterstorff. The volume also includes responses to each essay by Bas van Fraassen, Stephen Wykstra, David VanderLaan, Robin Collins, Raymond VanArragon, E. J. Coffman, Thomas Crisp, and Donald Smith. (shrink)

Like William James before him, Huw Price has influentially argued that truth has a normative role to play in our thought and talk. I agree. But Price also thinks that we should regard truth-conceived of as property of our beliefs-as something like a metaphysical myth. Here I disagree. In this paper, I argue that reflection on truth's values pushes us in a slightly different direction, one that opens the door to certain metaphysical possibilities that even a Pricean pragmatist can love.

Although Alston believed epistemically circular arguments were able to justify their conclusions, he was also disquieted by them. We will argue that Alston was right to be disquieted. We explain Alston’s view of epistemic circularity, the considerations that led him to accept it, and the purposes he thought epistemically circular arguments could serve. We then build on some of Alston’s remarks and introduce further limits to the usefulness of such arguments and introduce a new problem that stems from those limits. (...) The upshot is that adopting Alston’s view that epistemically circular arguments can be used to justify their conclusions is more costly than even he thought. (shrink)

What does truth have to do with freedom? That is, what is the relationship between our political and epistemic principles? In this paper, I grapple and reject Rorty's reasons for thinking that the former can't be based on the latter, but offer an alternative argument that supports his over-all conclusion that our epistemic and political values are ultimately intertwined.

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

In this essay we argue for the Janus-faced nature of hope. We show that attempts to sanitise the concept of hope either by separating it conceptually from other phenomena such as wishful thinking, or, more generally, by seeking to minimise the negative aspects of hope, do not help us to understand the nature of hope and its functions as regards religion. Drawing on functional accounts of religion from Clifford Geertz and Tamas Pataki, who both—in their different ways—see the function of (...) religion in terms of its capacity to satisfy deep psychological needs, we demonstrate that religion uniquely positions itself with regard to hope’s two faces, simultaneously exploiting positive and negative aspects of hope. (shrink)

This is a review of Foundations of Indirect Discrimination Law. Edited by Hugh Collins and Tarunabh Khaitan. [Oxford: Hart Publishing, 2018. x + 292 pp. Hardback £65.00. ISBN 978-15-09912-54-4.] Foundations of Indirect Discrimination Law. Edited by Hugh Collins and Tarunabh Khaitan. [Oxford: Hart Publishing, 2018. x + 292 pp. Hardback £65.00. ISBN 978-15-09912-54-4.].

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

Simon Blackburn has not shied away from the use of vivid imagery in developing, over a long and prolific career, a large-scale philosophical vision. Here one might think, for instance, of ‘Practical Tortoise Raising’ or ‘Ramsey's Ladder’ or ‘Frege's Abyss’. Blackburn develops a ‘quasi-realist’ account of many of our philosophical and everyday commitments, both theoretical (e.g., modality and causation) and practical (e.g., moral judgement and normative reasons). Quasi-realism aims to provide a naturalistic treatment of its targeted phenomena while earning the (...) right to deploy all of the ‘trappings’ of realism—i.e., while eschewing any idea that our normal thought and talk about such phenomena are pervasively in error. The quasi-realist project is that of explaining how (as Huw Price puts it here) ‘the folk come to “talk the realist talk” without committing ourselves—us theorists, as it were—to “walking the metaphysical walk”’ (p. 136). Quasi-realism, too, can speak of truth, facts, properties, belief, knowledge, and so on. The imagery in this collection also abounds, though, in capturing a different view of quasi-realism: No fewer than three of the contributors picture Blackburn as wanting to have his cake and eat it too (Louise Antony asking, in addition, ‘Who doesn't? It's cake’ [p. 19]). (shrink)

This paper, while neutral on questions about the minimality of truth, argues for the non-minimality of truth-aptness.

Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

Psychopathic behavior is characteristically amoral, but to date research studies have largely failed to identify any systematic differences in moral judgment capability between psychopaths and non-psychopaths. In this study, we investigate whether significant differences in moral judgment emerge when taking into account the phenotypic heterogeneity of the disorder through a well-validated distinction between psychopathic subtypes. Three groups of incarcerated participants [low-anxious psychopaths (n 1⁄4 12), high-anxious psychopaths (n 1⁄4 12) and non-psychopaths (n 1⁄4 24)] completed a moral judgment test involving (...) hypothet- ical dilemmas. The moral dilemmas featured personal (i.e. involving direct physical harm) or impersonal (i.e. involving indirect or remote harm) actions. Compared to non-psychopaths, both groups of psychopaths were significantly more likely to endorse the impersonal actions. However, only the low-anxious psychopaths were significantly more likely to endorse the personal harms when commission of the harm would maximize aggregate welfare the utilitarian choice. High-anxious psychopaths and non-psychopaths did not significantly differ in their personal moral judgments. These results provide novel laboratory evidence of abnormal moral judgment in psychopaths, as well as additional support for the importance of considering psychopathic subtypes. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

The flight to reference is a widely-used strategy for resolving philosophical issues. The three steps in a flight to reference argument are: (1) offer a substantive account of the reference relation, (2) argue that a particular expression refers (or does not refer), and (3) draw a philosophical conclusion about something other than reference, like truth or ontology. It is our contention that whenever the flight to reference strategy is invoked, there is a crucial step that is left undefended, and that (...) without a defense of this step, the flight to reference is a fatally flawed strategy; it cannot succeed in resolving philosophical issues. In this paper we begin by setting out the flight to reference strategy and explaining what is wrong with arguments that invoke the strategy. We then illustrate the problem by considering arguments for and against eliminative materialism. In the final section we argue that much the same problem undermines Philip Kitcher's attempt to defend scientific realism. (shrink)

It has been argued that Plato sought to make his rulers invulnerable to any kind of wrongdoing. In this paper we argue that this (humanly impossible) claim misunderstand the ways in which Plato shapes his state precisely in order to make the rulers safe from what could corrupt them.

Composite materialism, as I will understand it, is the view that human persons are composite material objects. This paper develops and investigates an argument, The Vague Singulars Argument, for the falsity of composite materialism. We shall see that cogent or not, the Vague Singulars Argument has philosophically significant ramifications.

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

Psychopathy, which is characterized by a constellation of antisocial behavioral traits, may be subdivided on the basis of etiology: “primary” (low-anxious) psychopathy is viewed as a direct consequence of some core intrinsic deficit, whereas “secondary” (high-anxious) psychopathy is viewed as an indirect consequence of environmental factors or other psychopathology. Theories on the neurobiology of psychopathy have targeted dysfunction within ventromedial prefrontal cortex (vmPFC) as a putative mechanism, yet the relationship between vmPFC function and psychopathy subtype has not been fully explored. (...) In this study, we administered two laboratory decision-making tasks (the Ultimatum Game and the Dictator Game) to a group of prisoners (n=47) to determine whether the different subtypes of psychopathy (primary vs. secondary) are associated with characteristic patterns of economic decision-making, and furthermore, whether either subtype exhibits similar performance to patients with vmPFC lesions. Comparing primary psychopaths (n=6) to secondary psychopaths (n=6) and non-psychopaths (n=22), we found that primary psychopathy was associated with significantly lower acceptance rates of unfair Ultimatum offers and lower offer amounts in the Dictator Game. Moreover, primary psychopaths were quantitatively similar to vmPFC lesion patients in their response patterns. These results support the purported connection between psychopathy and vmPFC dysfunction, bolster the distinction between primary and secondary psychopathy, and demonstrate the utility of laboratory economic decision-making tests in differentiating clinical subgroups. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

Three-dimensionalists , sometimes referred to as endurantists, think that objects persist through time by being “wholly present” at every time they exist. But what is it for something to be wholly present at a time? It is surprisingly difficult to say. The threedimensionalist is free, of course, to take ‘is wholly present at’ as one of her theory’s primitives, but this is problematic for at least one reason: some philosophers claim not to understand her primitive. Clearly the three-dimensionalist would be (...) better off if she could state her theory in terms accessible to all. We think she can. What is needed is a definition of ‘is wholly present at’ that all can understand. in this paper, we offer one. (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)

Tennenbaum's Theorem yields an elegant characterisation of the standard model of arithmetic. Several authors have recently claimed that this result has important philosophical consequences: in particular, it offers us a way of responding to model-theoretic worries about how we manage to grasp the standard model. We disagree. If there ever was such a problem about how we come to grasp the standard model, then Tennenbaum's Theorem does not help. We show this by examining a parallel argument, from a simpler model-theoretic (...) result. (shrink)

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among leaders in (...) the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (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)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

This book gathers the contribution of Brazilian and Argentine philosophers around themes of contemporary analytical philosophy.

The goal of the 2010 Ontology Summit was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these (...) recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (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 paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces (...) are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

This paper argues that Kant’s concept of ‘respect’ for the moral law has roots in Adam Smith’s concept of ‘regard’ for the general rules of conduct, which was translated as Achtung in the first German translation of the Theory of Moral Sentiments. After illustrating that Kant’s technical understanding of respect appeared relatively late in his intellectual development, I argue that Kant’s concept of respect and Smith’s concept of regard share a basic similarity: they are both a single complex (...) phenomenon with two core aspects, namely an attitude and a feeling. I then suggest that the concept of regard offered Kant a way to deal a problem concerning moral motivation that he was trying to solve at the time he likely first read Smith. I conclude by drawing some implications from the account I have offered for our understanding of Kant’s relation to Smith more generally. (shrink)

Palawan is a land of promise, and of paradox. On maps, it appears on the edge of the Philippines, isolated. Indeed, it is a kind of last frontier. Its population remained tiny for centuries, the government offering homestead land in the 1950s practically for free to attract migrants from outside. The Palawan State University was established by law in 1965, but did not become operational until 1972. A commercial airport did not exist until the 1980s, and for many years, flights (...) were limited. Yet Palawan is one of the oldest sites of human habitation in the Philippines with the famous Tabon Cave human fossils. The oldest bone fragment here has been dated to be about 47,000 years. We know, too, that trade with China goes back several centuries. Today, Palawan seems to be making up for lost time with new commercial investments pouring in at breakneck speed. In particular, outsiders have rediscovered its potentials around logging, mining, fisheries, and tourism. This has caused concern among individuals and civil society organizations who want sustainable development, and see the commercial developments mainly as extractive, not just of natural resources but of the human. There’s very cheap labor available. And when potential investors marvel about cheap land, they’re actually talking about displacing earlier settlers, including indigenous people, from their lands. A subtle but still insidious aspect of the exploitation of human resources is a transformation of the very concept of human development. Using the rhetoric of modernity, residents in Palawan are reorienting the way they view themselves as well as their families and friends. The value of a human being now hinges on how they look, and the desired appearance is defined from the outside, as we see in this anthology of research reports coming from the Chemical Youth project of the University of Amsterdam and the University of the Philippines Diliman. We read about the importance of fair skin as a projection of cleanliness, of high social status (meaning someone not engaged in manual labor and therefore not exposed to the sun). We read of how “femininity” is defined around body contours, and cosmetics, and how hormones are used by male-to-female transgenders. We go beyond the visual, reading about the importance of controlling or enhancing body odors among tour guides, who interestingly are especially concerned about the bad odor management of their foreign customers, using car perfumes to keep their work manageable and we learn how difficult it is for security guards to stay alert during their long shifts. Energy drinks and cigarettes help them perform their duties. All these transformations through what the French philosopher and historian Michel Foucault has called “technologies of the self” are as paradoxical as Palawan. On the surface, the products—which are technologies—seem to be mainly in the realm of the self but are, in reality, pushed, through marketing, from the outside, in contexts of inequality and exploitative labour relations. Personal aspirations are not personal but are for predefined standards of modernity, related to work-related demands and expectations. The self must be made presentable to the tourist, to the customers in malls, and to those who may threaten the properties that young people protect. It is not surprising that these transformations become problematic for the “self.” The skin whiteners, the hormones, the body deodorants, and the energy drinks are expensive and can distort budgetary priorities. The money for tonic drinks, for example, could well go into more nutritious food. The tragedy, too, many of the products used are of doubtful safety and efficacy. Even the energy drinks have much too high levels of caffeine that can cause cardiac palpitations. Cosmetics and the skin whiteners imported from China and unregistered with the Food and Drug Administration may contain toxic chemicals like mercury. But even registered skin whiteners can be problematic, their so-called “skin-whitening effect” coming about because they take away the upper layers of the skin, leaving behind a red glow (seen as “whitening”) which is actually inflammation. The whitened skin fails to protect against the sun, leading to adverse effects such as black spots. Ultimately though, the problems come with the very definition of the self. As the reports show, young people use the chemicals with some ambivalence, knowing how expensive they are and experiencing some of the undesirable side effects. There is, too, doubt about whether what they’re doing is indeed “good,” captured by how IP women will put on cosmetics only when they’re away from home and about to go to work. The cosmetics have to be removed before they return home because they are not socially acceptable. The research reports are not for Palawan alone. It must make us more critical and discerning as we revisit concepts of development and exploitation, modernity and tradition, self and community. The chemicals, in many ways, are like the products used in precolonial barter trade. For the Chinese, the beeswax and the sea cucumbers, for the inhabitants of Palawan the ceramics, represented faraway lands. To have those products gave prestige. Today, the skin whiteners and tonic drinks and other chemicals described in this anthology represent modernity with promises of not just of a more attractive self, but of better jobs, a better life. We are proud to have worked with the Palawan State University, and the people of Palawan, to gather powerful narratives that will now challenge the outside, the purveyors of modernity, to be more critical and discerning, the chemicals now to be seen not just as stuff applied to the biological body, but as powerful shapers of social bodies. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.