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 Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (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 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)

Moral particularism, on some interpretations, is committed to a shapeless thesis: the moral is shapeless with respect to the natural. (Call this version of moral particularism ‘shapeless moral particularism’). In more detail, the shapeless thesis is that the actions a moral concept or predicate can be correctly applied to have no natural commonality (or shape) amongst them. Jackson et al. (Ethical particularism and patterns, Oxford University Press, Oxford, 2000) argue, however, that the shapeless thesis violates the platitude ‘predication supervenes on (...) nature’—predicates or concepts apply because of how things are, and therefore ought to be rejected. I defend shapeless moral particularism by arguing that Jackson et al’s contention is less compelling than it firstly appears. My defense is limited in the sense that it does not prove shapeless moral particularism to be right and it leaves open the possibility that shapeless moral particularism might attract criticisms different from the ones advanced by Jackson et al. But at the very least, I hope to say enough to undermine Jackson et al’s powerful attack against it. The plan of this paper is as follows. Section 1 glosses the view of moral particularism and why it is taken to be essentially committed to the shapeless thesis. Section 2 examines a Wittgensteinian argument for the shapeless thesis. I shall argue that the Canberrans’ counter-arguments against it on grounds of disjunctive commonality and conceptual competence do not succeed. Section 3 explicates Canberrans’ predication supervenience argument against the shapeless thesis. Section 4 offers my criticisms of the Canberrans’ predication supervenience argument. In view of the above discussions, in Sect. 5, I conclude that there is no compelling argument (from the Canberrans) to believe that the shapeless thesis fails (as I have argued in Sect. 4). In fact, there is some good reason for us to believe it (as I have argued in Sect. 2). If so, I contend that moral particularism, when construed as essentially committed to the shapeless thesis, still remains as a live option. (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)

Governments standardly deploy a distinction between goods and services in assessing economic health and tracking national income statistics, of which medical goods and services carry significant importance. In what follows we draw on Basic Formal Ontology (BFO) to introduce a third kind of entity called patterns, which help capture the various ways in which goods and services are intertwined and help also to show how many services generate a new kind of non-goods-related products. Patterns are an overlooked yet essential features (...) of many economic sectors including medicine. Studying patterns offers new insights into various components of economic analysis, including outcomes-oriented evaluations of medical services and the value of human capital in the medical sphere. (shrink)

A realist theory of truth for a class of sentences holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar, we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The core of our theory is the (...) account of truthmaking for atomic sentences, in which we expose a pervasive ‘dogma of logical form’, which says that atomic sentences cannot have more than one truthmaker. In contrast to this, we uphold the mutual independence of logical and ontological complexity, and the authors outline formal principles of truthmaking taking account of both kinds of complexity. (shrink)

PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. The (...) purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. METHODS—We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. RESULTS—We introduced a new family of ‘lacks’ relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal U when p has no instance of U as part. Since p and U both exist, assertions involving ‘lacks_part’ and its cognates meet the requirements of positivity. CONCLUSION—By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied. (shrink)

The paradigm of referent tracking is based on a realist presupposition which rejects so-called negative entities (congenital absent nipple, and the like) as spurious. How, then, can a referent tracking-based Electronic Health Record deal with what are standardly called ‘negative findings’? To answer this question we carried out an analysis of some 748 sentences drawn from patient charts and containing some form of negation. Our analysis shows that to deal with these sentences we need to introduce a new ontological relationship (...) between a particular and a universal, which holds when no instance of the universal has a specific qualified ontological relation with the particular. This relation is found to be able to accommodate nearly all occurrences of negative findings in the examined sample, in ways which involve no reference to negative entities. (shrink)

Philosophy in the West divides into three parts: Analytic Philosophy (AP), Continental Philosophy (CP), and History of Philosophy (HP). But all three parts are in a bad way. AP is sceptical about the claim that philosophy can be a science, and hence is uninterested in the real world. CP is never pursued in a properly theoretical way, and its practice is tailor-made for particular political and ethical conclusions. HP is mostly developed on a regionalist basis: what is studied is determined (...) by the nation or culture to which a philosopher belongs, rather than by the objective value of that philosopher’s work. Progress in philosophy can only be attained by avoiding these pitfalls. (shrink)

Als zu Beginn des Jahrhunderts der Realismus wieder ernst genommen wurde, gab es viele Philosophen, die sich mit der Ontologie der Wahrheit befaßten. Unabhängig von der Bestimmung der Wahrheit als Korrespondenzbeziehung wollten sie herausfinden, inwieweit zur Erklärung der Wahrheit von Sätzen besondere Entitäten herangezogen werden müssen. Einige dieser Entitäten, so zum Beispiel Bolzanos ‘Sätze an sich’, Freges ‘Gedanken’ oder die ‘propositions’ von Russell und Moore, wurden als Träger der Eigenschaften Wahrheit und Falschheit aufgefaßt. Einige Philosophen jedoch, wie Russell, Wittgenstein im (...) ›Tractatus‹ und Husserl in den ›Logischen Untersuchungen‹, argumentierten, zusätzlich zu den Wahrheitsträgern bzw. an ihrer Stelle müßten Entitäten angenommen werden, auf Grund deren Sätze und/oder ‘Propositionen’ wahr sind. Solchen Entitäten gab man verschiedene Namen, insbesondere ‘fact’, ‘Tatsache’, ‘state of affairs’ und ‘Sachverhalt’. 1 Wir wollen einer Entscheidung über die Angebrachtheit dieser Ausdrücke nicht vorgreifen und daher zunächst eine neutralere Terminologie verwenden: Alle Entitäten, die für diese zweite Rolle in Frage kommen, wollen wir ‘Wahrmacher’ nennen. (shrink)

French translation of "Truth-Makers" (1984). A realist theory of truth for a class of sentence holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The core (...) of our theory is the account of truthmaking for atomic sentences, in which we expose a pervasive ‘dogma of logical form’, which says that atomic sentences cannot have more than one truthmaker. The authors uphold the mutual independence of logical and ontological complexity. The theory is compared with that of Wittgenstein’s Tractatus, and the authors outline formal principles of truthmaking taking account of both kinds of complexity and suggesting how to overcome Wittgenstein’s problem of negation. (shrink)

The British philosopher Michael Dummett (1925–2011) not only had a massive influence on the development of analytical philosophy within the philosophy of language, philosophy of mathematics, and metaphysics, but also contributed significantly to historical and metaphilosophical debates about the nature of this philosophical movement and its proper account. He proposed to define analytical philosophy as philosophy whose aim is the analysis of the structure of thought by way of the analysis of language. Hence, it is philosophy the gist of (...) which is the linguistic turn. A number of critics of this proposal (including Barry Smith, Peter Hylton, and Hans-Johann Glock) emphasised that Dummett’s proposal captures merely some features of this diversified and multifaceted philosophical tradition, and is far from being historically adequate. (shrink)

We propose a definition of capability as a class intermediate between function and disposition as the latter are defined in Basic Formal Ontology (BFO). A disposition inheres in a material entity and is realized in a certain kind of process. An example is the disposition of a glass to break when struck, which is realized when it shatters. A function is a disposition which is (simply put) the rationale for the existence of its bearer. To say for example that a (...) water pump has the function to pump water is to say that the pump exists because something was needed that would pump water. Capabilities are a special sort of disposition in that that, like functions, they can be evaluated on the basis of how well they are realized. They differ from functions in that their realizations are not the rationale – not the primary reason – for the existence of their bearers. Thus, a water pump may have many capabilities, including to be weatherproof, to run without lubricant, and so forth, but only one function. All functions are capabilities on the view we defend, but not all capabilities are functions. We develop a series of axioms to distinguish capabilities formally from both dispositions and functions and provide examples of the use of ‘capability’ in a variety of domains. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

This paper presents the Obstetric and Neonatal Ontology (OntONeo). This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data and to serve interoperability of the associated data and information systems. More generally, it will serve interoperability of clinical and translational data, for example deriving from genomics disciplines and from clinical trials. Interoperability of EHR data is important to ensuring continuity of care during the prenatal and postnatal periods for both mother and child. As (...) a strategy to advance such interoperability we use an approach based on ontological realism and on the ontology development principles of the Open Biomedical Ontologies Foundry, including reuse of reference ontologies wherever possible. We describe the structure and coverage domain of OntONeo and the process of creating and maintaining the ontology. (shrink)

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)

Batı’da teorik felsefe; Analitik Felsefe (AF), Kıta Felsefesi (KF) ve Felsefe Tarihi (FT) olmak üzere üçe ayrılır. Fakat üçünde de işler yolunda değildir. AF, felsefenin bir bilim olabileceği iddiasından kuşku duyduğu için gerçek dünyayla ilgilenmiyorken başından beri uygun bir teorik yöntem izlemeyen Kıta Felsefesinin uygulanışı, belirli politik ve etik yargılara hizmet edecek şekilde özelleştirilmiştir. FT çalışmalarının gidişatı ise eldeki eserin nesnel değerinden daha çok ilgili filozofun ait olduğu ulus veya kültüre göre bölgesel bir temelde gelişmiştir. Felsefede ilerleme sağlanacaksa bu ancak (...) bahsi geçen tuzaklardan kaçınılarak gerçekleşebilir. (shrink)

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

White progressives in the U.S. are currently experiencing two profound reckonings that typically are assumed to be unrelated. On the one hand, the Dobbs verdict overturned the assumption that the right to choose with respect to abortion is too socially entrenched, juridically settled, or politically sacred to be denied. On the other hand, climatological conditions of possibility for comfortable existence are increasingly under threat in locales in which residents have come to expect to enjoy secure lives and livelihoods. This essay (...) highlights what Indigenous communities across the U.S. already know well. Namely, threats to reproductive freedom and climate crisis are neither new nor separable. Both phenomena have common colonial roots that continue to proliferate. Each is a result of the disruption and destruction of Indigenous kinship assemblages. Indeed, in aiming to remediate their current reckonings, white progressives routinely (if unthinkingly) support forms of settler state violence that perpetuate reproductive and climate injustice in Indigenous communities. We appeal to white progressives, notably including white feminists, to embrace the proposition that their reckonings cannot be properly understood, nor successfully addressed without prioritizing Indigenous futurity. We call for centering forms of Indigenous feminist praxis that facilitate robust Indigenous coalitions of anti-colonial resistance. (shrink)

When governments collect data relating to economic activity they commonly employ a distinction between goods and services. Both goods and services have economic value. Goods (cars, houses, bottles of milk) are, very roughly, independent continuants which can be alienated (sold, gifted, rented, and so forth). Services (hairdressing, gardening, teaching) are, again very roughly, occurrents. They are occurrents which are further often said to be marked by the fact that production and consumption coincide. Social services under both headings typically involve combinations (...) of service provision. The patterns in question are primarily those of the family (where the patterns to be maintained or restored are, roughly, those characteristic of a healthy family life) and of the child (patterns characteristic of healthy development, provided by child protective services, who work to prevent child abuse). (shrink)

Historically, scientific and engineering expertise has been key in shaping research and innovation policies, with benefits presumed to accrue to society more broadly over time. But there is persistent and growing concern about whether and how ethical and societal values are integrated into R&I policies and governance, as we confront public disbelief in science and political suspicion toward evidence-based policy-making. Erosion of such a social contract with science limits the ability of democratic societies to deal with challenges presented by new, (...) disruptive technologies, such as synthetic biology, nanotechnology, genetic engineering, automation and robotics, and artificial intelligence. Many policy efforts have emerged in response to such concerns, one prominent example being Europe's Eighth Framework Programme, Horizon 2020, whose focus on “Responsible Research and Innovation” provides a case study for the translation of such normative perspectives into concrete policy action and implementation. Our analysis of this H2020 RRI approach suggests a lack of consistent integration of elements such as ethics, open access, open innovation, and public engagement. On the basis of our evaluation, we suggest possible pathways for strengthening efforts to deliver R&I policies that deepen mutually beneficial science and society relationships. (shrink)

I distinguish paradoxes and hypodoxes among the conundrums of time travel. I introduce ‘hypodoxes’ as a term for seemingly consistent conundrums that seem to be related to various paradoxes, as the Truth-teller is related to the Liar. In this article, I briefly compare paradoxes and hypodoxes of time travel with Liar paradoxes and Truth-teller hypodoxes. I also discuss Lewis’ treatment of time travel paradoxes, which I characterise as a Laissez Faire theory of time travel. Time travel paradoxes are impossible according (...) to Laissez Faire theories, while it seems hypodoxes are possible. (shrink)

We often talk and behave as if being a man required more than just being male, and being a woman required more than just being female. There are expectations that need to be met if someone wants to fully qualify as a man or a woman in their social environment, expectations regarding their behaviour as well as character. It is, however, not entirely obvious what ‘being a man’ or ‘being a woman’ actually means and in what way and to what (...) extent it defines our identity, making us who we are. Would I be a different person if I were a woman? And what would it take for me to be a woman? Could I conceivably be neither? Or both? If gender were nothing but sex, telling a man to ‘be a man’ would make little sense. We may have different ideas about what it means to be a man or woman and how we need to behave in order to secure or maintain our manhood or womanhood, but we are all likely to have some deeply ingrained understanding of what makes a man a man and a woman a woman that goes beyond mere biology. Does it, however, follow that gender can, if necessary or desired, be completely detached from sex, that I can be a woman despite having all the physical attributes of a male member of my species, or a man despite being biologically female? If so, on what grounds exactly would we decide who is what? (shrink)

When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be (...) aligned with joint doctrine. It requires also that the separate information systems used by the different elements of a joint force must be interoperable, in the sense that data and information that is generated by each element must be usable (understandable, processable) by all the other elements that need them. Currently, such interoperability is impeded by multiple inconsistencies among the different data and software standards used by warfighters. We describe here the on-going project of creating a Joint Doctrine Ontology (JDO), which uses joint doctrine to provide shared computer-accessible content valid for any field of military endeavor, organization, and information system. JDO addresses the two previously mentioned requirements of unified action by providing a widely applicable benchmark for use by developers of information systems that will both guarantee alignment with joint doctrine and support interoperability. (shrink)

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata registries, (...) thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning. (shrink)

A letter to The Times of London, May 9, 1992 protesting the Cambridge University proposal to award an honorary degree to M. Jacques Derrida.

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)

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)

The main message of the paper is that there is a disconnect between what many philosophers of mind think of as the scientific practice of reductive or reductionist explanation, and what the most relevant scientific work is actually like. I will sketch what I see as a better view, drawing on various ideas in recent philosophy of science. I then import these ideas into the philosophy of mind, to see what difference they make.1 At the end of the paper I (...) address a possible objection: the familiar package of ideas I reject in the philosophy of science should not be lightly discarded, because other popular views on fundamental issues depend on positions that I want to reject. I reply that those apparently attractive further ideas are not worth holding onto. (shrink)

The book presents the first comprehensive survey of limits of the intentional control of action from an interdisciplinary perspective. It brings together leading scholars from philosophy, psychology, and the law to elucidate this theoretically and practically important topic from a variety of theoretical and disciplinary approaches. It provides reflections on conceptual foundations as well as a wealth of empirical data and will be a valuable resource for students and researchers alike. Among the authors: Clancy Blair, Todd S. Braver, Michael (...) W. Cole, Anika Fäsche, Maayan Davidov, Peter Gollwitzer, Kai Robin Grzyb, Tobias Heikamp, Gabriele Oettingen, Rachel McKinnon, Nachschon Meiran, Hans Christian Röhl, Michael Schmitz, John R. Searle, Gottfried Seebaß, Gisela Trommsdorff, Felix Thiede, J. Lukas Thürmer, Frank Wieber. (shrink)

Experimental philosophers have gathered impressive evidence for the surprising conclusion that philosophers' intuitions are out of step with those of the folk. As a result, many argue that philosophers' intuitions are unreliable. Focusing on the Knobe Effect, a leading finding of experimental philosophy, we defend traditional philosophy against this conclusion. Our key premise relies on experiments we conducted which indicate that judgments of the folk elicited under higher quality cognitive or epistemic conditions are more likely to resemble those of the (...) philosopher. We end by showing how our experimental findings can help us better understand the Knobe Effect. (shrink)

We present a dynamic model of the evolution of communication in a Lewis signaling game while systematically varying the degree of common interest between sender and receiver. We show that the level of common interest between sender and receiver is strongly predictive of the amount of information transferred between them. We also discuss a set of rare but interesting cases in which common interest is almost entirely absent, yet substantial information transfer persists in a *cheap talk* regime, and offer a (...) diagnosis of how this may arise. -/- . (shrink)

The three young philosophers Kevin Mulligan, Peter Simons and Barry Smith have become well-known in the last few years especially in German-speaking analytical philosophy and phenomenology circles. This is on the one hand as a result of their historical and systematic philosophical work; but it is also because of the provocative way in which they represent their philosophy. Because they often appear in threes, they have become known as the "gang of three" or "three musketeers" or even – (...) and this in an admiring sense – "mafiosi" (Rescher). They are known primarily for the small workshops they have been organizing in uncomplicated Anglo-Saxon manner all over Europe. Their goal has been to show that analytic philosophy as it has been pursued up to now is in need of reform and also that the history of scientific philosophizing is not identical to the history of Anglo-Saxon analytic philosophy. Above all, they have tried to make more well known the Austrian tradition of scientific philosophy, and they can be given credit for having done much to promote the current interest in this tradition, which means: the history of Austrian philosophy of the 19th and early 20th centuries and its historical context in the Austro-Hungarian Empire. (shrink)

In recent years, language has been shown to play a number of important cognitive roles over and above the communication of thoughts. One hypothesis gaining support is that language facilitates thought about abstract categories, such as democracy or prediction. To test this proposal, a novel set of semantic memory task trials, designed for assessing abstract thought non-linguistically, were normed for levels of abstractness. The trials were rated as more or less abstract to the degree that answering them required the participant (...) to abstract away from both perceptual features and common setting associations corresponding to the target image. The normed materials were then used with a population of people with aphasia to assess the relationship of abstract thought to language. While the language-impaired group with aphasia showed lower overall accuracy and longer response times than controls in general, of special note is that their response times were significantly longer as a function of a trial’s degree of abstractness. Further, the aphasia group’s response times in reporting their degree of confidence (a separate, metacognitive measure) were negatively correlated with their language production abilities, with lower language scores predicting longer metacognitive response times. These results provide some support for the hypothesis that language is an important aid to abstract thought and to metacognition about abstract thought. (shrink)

This paper’s aim is to provide overview of the punishment of war crimes. It considers first the rationale of the law of war, the identification and scope of war crimes, and proceeds to consider the justification of punishing war crimes, arguing for a consequentialist view with side-constraints. It then considers the alternative of reconciliation.

Understanding everyday behavior relies heavily upon understanding our ability to improvise, how we are able to continuously anticipate and adapt in order to coordinate with our environment and others. Here we consider the ability of musicians to improvise, where they must spontaneously coordinate their actions with co-performers in order to produce novel musical expressions. Investigations of this behavior have traditionally focused on describing the organization of cognitive structures. The focus, here, however, is on the ability of the time-evolving patterns of (...) inter-musician movement coordination as revealed by the mathematical tools of complex dynamical systems to provide a new understanding of what potentiates the novelty of spontaneous musical action. We demonstrate this approach through the application of cross wavelet spectral analysis, which isolates the strength and patterning of the behavioral coordination that occurs between improvising musicians across a range of nested time-scales. Revealing the sophistication of the previously unexplored dynamics of movement coordination between improvising musicians is an important step towards understanding how creative musical expressions emerge from the spontaneous coordination of multiple musical bodies. (shrink)

Despite the ubiquity of inner speech in our mental lives, methods for objectively assessing inner speech capacities remain underdeveloped. The most common means of assessing inner speech is to present participants with tasks requiring them to silently judge whether two words rhyme. We developed a version of this task to assess the inner speech of a population of patients with aphasia and corresponding language production deficits. As expected, patients’ performance on the silent rhyming task was severely impaired relative to controls. (...) More surprisingly, however, patients’ performance on this task did not correlate with their performance on a variety of other standard tests of overt language abilities. In particular, patients who were generally unimpaired in their abilities to overtly name objects during confrontation naming tasks, and who could reliably judge when two words spoken to them rhymed, were still severely impaired (relative to controls) at completing the silent rhyme task. This seems to suggest that inner speech was more severely impaired in these patients than outer speech. However, these results should also cause us to critically reflect on the relation between inner speech and silent rhyme judgments more generally. (shrink)

This study examines the relation of language use to a person’s ability to perform categorization tasks and to assess their own abilities in those categorization tasks. A silent rhyming task was used to confirm that a group of people with post-stroke aphasia (PWA) had corresponding covert language production (or “inner speech”) impairments. The performance of the PWA was then compared to that of age- and education-matched healthy controls on three kinds of categorization tasks and on metacognitive self-assessments of their performance (...) on those tasks. The PWA showed no deficits in their ability to categorize objects for any of the three trial types (visual, thematic, and categorial). However, on the categorial trials, their metacognitive assessments of whether they had categorized correctly were less reliable than those of the control group. The categorial trials were distinguished from the others by the fact that the categorization could not be based on some immediately perceptible feature or on the objects’ being found together in a type of scenario or setting. This result offers preliminary evidence for a link between covert language use and a specific form of metacognition. (shrink)

This paper explores relationships between environment and education after the Covid-19 pandemic through the lens of philosophy of education in a new key developed by Michael Peters and the Philosophy of Education Society of Australasia. The paper is collectively written by 15 authors who responded to the question: Who remembers Greta Thunberg? Their answers are classified into four main themes and corresponding sections. The first section, ‘As we bake the earth, let's try and bake it from scratch’, gathers wider (...) philosophical considerations about the intersection between environment, education, and the pandemic. The second section, ‘Bump in the road or a catalyst for structural change?’, looks more closely into issues pertaining to education. The third section, ‘If you choose to fail us, we will never forgive you’, focuses to Greta Thunberg’s messages and their responses. The last section, ‘Towards a new normal’, explores future scenarios and develops recommendations for critical emancipatory action. The concluding part brings these insights together, showing that resulting synergy between the answers offers much more then the sum of articles’ parts. With its ethos of collectivity, interconnectedness, and solidarity, philosophy of education in a new key is a crucial tool for development of post-pandemic education. (shrink)

Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present how (...) an ontology for the obstetric and neonatal domain deals with these general elements documented in health care encounters. Our goal is to promote the interoperability of information among EHRs created in different specialties. To develop our ontology, we used two main approaches: one based on ontological realism, the other based on the principles of the OBO Foundry, including reuse of reference ontologies. (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)