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)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

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)

Self-knowledge is the focus of considerable attention from philosophers: Knowing Our Own Minds gives a much-needed overview of current work on the subject, bringing together new essays by leading figures. Knowledge of one's own sensations, desires, intentions, thoughts, beliefs, and other attitudes is characteristically different from other kinds of knowledge: it has greater immediacy, authority, and salience. The contributors examine philosophical questions raised by the distinctive character of self-knowledge, relating it to knowledge of other minds, to rationality and agency, externalist (...) theories of psychological content, and knowledge of language. Together these original, stimulating, and closely interlinked essays demonstrate the special relevance of self-knowledge to a broad range of issues in epistemology, philosophy of mind, and philosophy of language. (shrink)

A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.

The idea that appearances provide justifications for beliefs—the principle of phenomenal conservatism—is self-evidently true. In the case of cognitive penetration, however, it seems that certain irrational etiologies of a belief may influence the epistemic quality of that belief. Susanna Siegel argues that these etiologies lead to ‘epistemic downgrade.’ Instead of providing us with a decisive objection, cognitive penetration calls for us to clarify our epistemic framework by understanding the formative parts of appearances. In doing so, the two different but inseparable (...) ideas of sensation and intellection provide us with a basis of our appearances. These appearances, in turn, provide us with the objective evidence needed to test our judgements. Thus, the extra-sensory concepts of intellectual identification and the appearances they help form become an epistemic groundwork. (shrink)

Biological molecules such as enzymes and antibodies display a unique capacity to recognize and respond to other molecules in a way which can be exploited in the development of analytical devices. In a biosensor, the biological recognition system creates a physiochemical change proximal to a suitable transducer and thereby converts the concentration of the analyte into a quantifiable electrical signal. The design and construction of these devices requires an imaginative combination of biological, chemical, physical and engineering disciplines. Biosensors will find (...) application in a variety of analytical fields. (shrink)

"... chronicles the story of U.G. Krishnamurti, the Cosmic Naxalite, from his troubled childhood to his disillusionment with many of the leading spiritual teachers of the twentieth century and his catastrophic personal life. In 1967, UG underwent a series of biological mutations that left him in the 'natural state'--functioning without the interference of thought. With no fixed address, no followers and no organization, UG spent the next thirty years travelling the world with an uncompromising message: that 'mind is a myth' (...) and dthe human condition should be demystified and de-psyhologized and viewed in purely physiological terms."--Cover. (shrink)

Brickhouse and Smith cast new light on Plato's early dialogues by providing novel analyses of many of the doctrines and practices for which Socrates is best known. Included are discussions of Socrates' moral method, his profession of ignorance, his denial of akrasia, as well as his views about the relationship between virtue and happiness, the authority of the State, and the epistemic status of his daimonion.

Socrates' moral psychology is widely thought to be 'intellectualist' in the sense that, for Socrates, every ethical failure to do what is best is exclusively the result of some cognitive failure to apprehend what is best. Until publication of this book, the view that, for Socrates, emotions and desires have no role to play in causing such failure went unchallenged. This book argues against the orthodox view of Socratic intellectualism and offers in its place a comprehensive alternative account that explains (...) why Socrates believed that emotions, desires and appetites can influence human motivation and lead to error. Thomas C. Brickhouse and Nicholas D. Smith defend the study of Socrates' philosophy and offer an alternative interpretation of Socratic moral psychology. Their novel account of Socrates' conception of virtue and how it is acquired shows that Socratic moral psychology is considerably more sophisticated than scholars have supposed. (shrink)

Thomas Brickhouse and Nicholas Smith offer a comprehensive historical and philosophical interpretation of, and commentary on, one of Plato's most widely read works, the Apology of Socrates. Virtually every modern interpretation characterizes some part of what Socrates says in the Apology as purposefully irrelevant or even antithetical to convincing the jury to acquit him at his trial. This book, by contrast, argues persuasively that Socrates offers a sincere and well-reasoned defense against the charges he faces. First, the authors establish (...) a consensus of ancient reports about Socrates ' moral and religious principles and show that these prohibit him from needlessly risking the condemnation of the jury. Second, they consider each specific claim made by Socrates in the Apology and show how each can be construed as an honest effort to inform the jurors of the truth and to convince them of his blamelessness. The arguments of this book are informed by a critical review of the scholarly literature and careful attention to the philosophy expressed in Plato's other early dialogues. (shrink)

Socrates' moral psychology is widely thought to be 'intellectualist' in the sense that, for Socrates, every ethical failure to do what is best is exclusively the result of some cognitive failure to apprehend what is best. Until publication of this book, the view that, for Socrates, emotions and desires have no role to play in causing such failure went unchallenged. This book argues against the orthodox view of Socratic intellectualism and offers in its place a comprehensive alternative account that explains (...) why Socrates believed that emotions, desires and appetites can influence human motivation and lead to error. Thomas C. Brickhouse and Nicholas D. Smith defend the study of Socrates' philosophy and offer an alternative interpretation of Socratic moral psychology. Their novel account of Socrates' conception of virtue and how it is acquired shows that Socratic moral psychology is considerably more sophisticated than scholars have supposed. (shrink)

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

Health promotion involves social and environmental interventions designed to benefit and protect health. It often harmfully impacts the environment through air and water pollution, medical waste, g...

Sound propagation within certain non-relativistic condensed matter models obeys a relativistic wave equation despite such systems admitting entirely non-relativistic descriptions. A natural question that arises upon consideration of this is, “do devices exist that will experience the relativity in these systems?” We describe a thought experiment in which ‘acoustic observers’ possess devices called sound clocks that can be connected to form chains. Careful investigation shows that appropriately constructed chains of stationary and moving sound clocks are perceived by observers on the (...) other chain as undergoing the relativistic phenomena of length contraction and time dilation by the Lorentz factor, \, with \ the speed of sound. Sound clocks within moving chains actually tick less frequently than stationary ones and must be separated by a shorter distance than when stationary to satisfy simultaneity conditions. Stationary sound clocks appear to be length contracted and time dilated to moving observers due to their misunderstanding of their own state of motion with respect to the laboratory. Observers restricted to using sound clocks describe a universe kinematically consistent with the theory of special relativity, despite the preferred frame of their universe in the laboratory. Such devices show promise in further probing analogue relativity models, for example in investigating phenomena that require careful consideration of the proper time elapsed for observers. (shrink)

Recent work by Peijnenburg, Atkinson, and Herzberg suggests that infinitists who accept a probabilistic construal of justification can overcome significant challenges to their position by attending to mathematical treatments of infinite probabilistic regresses. In this essay, it is argued that care must be taken when assessing the significance of these formal results. Though valuable lessons can be drawn from these mathematical exercises (many of which are not disputed here), the essay argues that it is entirely unclear that the form of (...) infinitism that results meets a basic requirement: namely, providing an account of infinite chains of propositions qua reasons made available to agents. (shrink)

In Plato’s Protagoras, Socrates clearly indicates that he is a cognitivist about the emotions—in other words, he believes that emotions are in some way constituted by cognitive states. It is perhaps because of this that some scholars have claimed that Socrates believes that the only way to change how others feel about things is to engage them in rational discourse, since that is the only way, such scholars claim, to change another’s beliefs. But in this paper we show that Socrates (...) is also responsive to, and has various non-rational strategies for dealing with, the many ways in which emotions can cloud our judgment and lead us into poor decision-making. We provide an account of how Socrates can consistently be a cognitivist about emotion and also have more than purely rational strategies for dealing with emotions. (shrink)

In the Protagoras, Socrates argues that each of the virtue-terms refers to one thing (: 333b4). But in the Laches (190c8–d5, 199e6–7), Socrates claims that courage is a proper part of virtue as a whole, and at Euthyphro 11e7–12e2, Socrates says that piety is a proper part of justice. But A cannot be both identical to B and also a proper part of B – piety cannot be both identical to justice and also a proper part of justice. In this (...) paper we argue that coherent sense can be made of Socrates'' apparently conflicting claims. The key to understanding Socrates'' position, we will argue, is the central role of wisdom among the virtues. It is through the relationship of each virtue to wisdom that each may be said to be the same as all of the others, on the one hand, and also that some virtues may be regarded as proper parts of some other virtues, or as proper parts of virtue in general, on the other. (shrink)

In this paper we argue that Socrates is a cognitivist about emotions, but then ask how the beliefs that constitute emotions can come into being, and why those beliefs seem more resistant to change through rational persuasion than other beliefs.

Political corruption imposes substantial costs on shareholders in the U.S. Yet, we understand little about the basic factors that exacerbate or mitigate the value consequences of political corruption. Using federal corruption convictions data, we find that firm-level economic rents and monitoring mechanisms moderate the negative relation between corruption and firm value. The value consequences of political corruption are exacerbated for firms operating in low-rent product markets and mitigated for firms subject to external monitoring by state governments or monitoring induced by (...) disclosure transparency. Our results should inform managers and policymakers of the tradeoffs imposed on firms operating in politically corrupt districts. (shrink)

Glowacki defines peace as harmonious relationships between groups maintained without the threat of violence, where groups can be anything from families to nation states. However, defining such contentious concepts like “peace” and “groups” is a difficult task, and we discuss the implications of Glowacki's definitions for understanding intergroup relationships and their evolutionary history.

Pojęcie niszy (otoczenia, kontekstu, siedliska, środowiska) nie cieszy się specjalnym zainteresowaniem ontologów, mimo że ma szerokie zastosowanie w rozmaitych dyscyplinach, od biologii ewolucyjnej po ekonomię. Niniejszy artykuł zawiera pierwszą teorię formalną tego pojęcia — teorię relacji pomiędzy przedmiotami a ich niszami. Teoria ta opiera się na istniejącym dorobku mereologii, topologii i teorii lokalizacji przestrzennej, które są narzędziami ontologii formalnej. Jest ona tutaj ilustrowana głównie za pomocą prostych przykładów z biologii, ale pojęcie niszy należy rozumieć — podobnie jak pojęcia części, granicy (...) i położenia — jako pojęcie strukturalne, znajdujące zastosowanie w obszernym zakresie różnych dziedzin. (shrink)

Oxford Studies in Ancient Philosophy is an annual publication which includes original articles on a wide range of topics in ancient philosophy, and review articles of major books. In this supplementary volume, a number of renowned scholars of Plato reflect upon their interpretative methods. Topics covered include the use of ancient authorities in interpreting Plato's dialogues, Plato's literary and rhetorical style, his arguments and characters, and his use of the dialogue form. The collection is not intended as a comprehensive survey (...) of methodological approaches; rather it offers a number of different perspectives and clearly articulated interpretations by leading scholars in the field. (shrink)

In his interrogation of Meletus in Plato’s version of Socrates’ defense speech, Socrates offers an interesting argument that promises to provide important evidence for his views about crime and punishment—if only we can understand how the argument is supposed to work. It is our project in this paper to do that. We argue that there are two main problems with the argument: one is that it is not obvious how to make the argument valid; the other is that the argument (...) seems to rely on a distinction that Socrates himself rejects ––a distinction between voluntary and involuntary wrongdoing. Earlier discussions of the argument require Socrates to be using a premise here that he regards as false. In this paper, we argue that Socrates actually regards the critical premise as true, and thus we end up providing a significantly new interpretation of Socrates’ view that all wrongdoing is involuntary. We claim, that even this position must accommodate the idea that some people really do voluntary harm to others. (shrink)

We here analyse the ethical dimensions of the UK's ‘Research Excellence Framework’, the latest version of an exercise which assesses the quality of university research in the UK every seven or so years. We find many of the common objections to this exercise unfounded, such as that it is excessively expensive by comparison with alternatives such as various metrics, or that it turns on the subjective judgement of the assessors. However there are grounds for concern about the crude language in (...) which for example all relevant scholarship becomes called ‘research’ and publications become ‘outputs’. The focus on the impact of research, which was a new feature of the most recent exercise, is particularly problematic, creating as it does a tendency to what Aristotle called alazony, self-aggrandisement, on the part of academics. We conclude that the REF is a mixed good from an ethical point of view, and that more could be done to mitigate its more unfortunate features. (shrink)

Socrates is one of the most important yet enigmatic philosophers of all time; his fame has endured for centuries despite the fact that he never actually wrote anything. In 399 B.C.E., he was tried on the charge of impiety by the citizens of Athens, convicted by a jury, and sentenced to death (ordered to drink poison derived from hemlock). About these facts there is no disagreement. However, as the sources collected in this book and the scholarly essays that follow them (...) show, several of even the most basic facts about these events were controversial in antiquity, and the questions persist today: How and why was Socrates brought to trial? Why did the jurors, members of the world's first democracy, find him guilty? When he was given an opportunity to escape execution, why did he refuse to do so and instead accept the punishment that he and his friends agreed was unjustly assigned to him? How exactly did Socrates die? Differences of opinion on these and other issues continue to arouse our curiosity and to challenge new generations of students and scholars. The Trial and Execution of Socrates: Sources and Controversies is the first work to collect in one place all of the major ancient sources on Socrates' death--those of both his critics and his defenders--as well as recent scholarly views. Part I includes new translations of Plato's Euthyphro, Apology, Crito, and the death scene from Phaedo, as well as other ancient sources that shed light on Socrates' trial and execution. Part II features some of the most influential recent scholarship on this historically momentous event with work by M. F. Burnyeat, Robert Parker, Mark L. McPherran, Thomas C. Brickhouse and Nicholas D. Smith, Richard Kraut, Christopher Gill, and Enid Bloch (whose essay is published here for the first time). Ideal for undergraduate surveys of ancient Greek philosophy and upper-level courses on Socrates and Socratic philosophy, this unique collection provides an unprecedented look into the many perplexing questions surrounding the trial and execution of this remarkable man. (shrink)