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)

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)

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)

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)

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)

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.

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)

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)

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.

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)

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.

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)

A contemporary of William Shakespeare and Ben Jonson, Christopher Marlowe was one of the most influential early modern dramatists, whose life and mysterious death have long been the subject of critical and popular speculation. This collection sets Marlowe's plays and poems in their historical context, exploring his world and his wider cultural influence. Chapters by leading international scholars discuss both his major and lesser-known works. Divided into three sections, 'Marlowe's works', 'Marlowe's world', and 'Marlowe's reception', the book ranges from Marlowe's (...) relationship with his own audience through to adaptations of his plays for modern cinema. Other contexts for Marlowe include history and politics, religion and science. Discussions of Marlowe's critics and Marlowe's appeal today, in performance, literature and biography, show how and why his works continue to resonate; and a comprehensive further reading list provides helpful suggestions for those who want to find out more. (shrink)

Original essays by philosophers of language and philosophers of time exploring the semantics and metaphysics of tense.

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)

The claim that the citizen's duty is to “persuade or obey” the laws, expressed by the personified Laws of Athens in Plato's Crito, continues to receive intense scholarly attention. In this article, we provide a general review of the debates over this doctrine, and how the various positions taken may or may not fit with the rest of what we know about Socratic philosophy. We ultimately argue that the problems scholars have found in attributing the doctrine to Socrates derive from (...) an anachronistic and erroneous understanding of Socrates as a kind of libertarian. (shrink)

There has been little scholarly attention given to explaining exactly how and why Socrates thinks that wrongdoing damages the soul. But there is more than a simple gap in the literature here, we shall argue. The most widely accepted view of Socratic moral psychology, we claim, actually leaves this well-known feature of Socrates’ philosophy absolutely inexplicable. In the first section of this paper, we rehearse this view of Socratic moral psychology, and explain its inadequacy on the issue of the damaging (...) consequences of wrongdoing. We then go on to provide our own account of the way in which injustice damages the soul, and then draw conclusions about how Socratic moral psychology should be understood. (shrink)

In this paper we explore plato's paradoxical remarks about the philosophical rulers' use of dishonesty in the "republic"--Rulers who, On the one hand, Are said to love truth above all else, But on the other hand are encouraged to make frequent use of "medicinal lies." we establish first that plato's remarks are in fact consistent, According to the relevant platonic theories too often forgotten by both critics and defenders of plato. Finally, We reformulate the underlying moral issue of the purported (...) right not to be lied to, And its alternative in platonic political philosophy: paternalism. (shrink)

After he has been condemned to death, Socrates spends a few minutes talking to the jurors before he is taken away. First, he rebukes those who voted against him for resorting to using the court to kill him when they could have waited and let nature do the same job very soon anyhow, for Socrates is an old man. He next contrasts the evils to which his accusers have resorted to his own unbending resolve never to resort to shameful actions, (...) even though in this case such things might have saved his life. Then he prophesies to those jurors that younger men will make their lives far more difficult than ever Socrates did, and thus strips from them any notion they may have had that they gained anything by condemning him. (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.

: In her recent paper, “How to Escape Indictment for Impiety: Teaching as Punishment in the Euthyphro,” G. Fay Edwards argues that if Socrates were to become Euthyphro’s student, this should count as the appropriate punishment for Socrates’ alleged crime. In this paper, we show that the interpretation Edwards has proposed conflicts with what Socrates has to say about the functional role of punishment in the Apology, and that the account Socrates gives in the Apology, properly understood, also provides the (...) correct interpretation of what Socrates says in the Euthyphro about the role of instruction for wrongdoers. (shrink)

In this paper, we defend Socratic studies as a research programme against several recent attacks, including at least one recently published in Polis . Critics have argued that the study of Socrates, based upon evidence mostly or entirely derived from some set of Plato's dialogues, is founded upon faulty and indefensible historical or hermeneutical technique. We begin by identifying what we believe are the foundational principles of Socratic studies, as the field has been pursued in recent years, and we then (...) show how the research programme that derives from accepting these principles is not defeated by any of the most common recent criticisms of it. Specifically, we argue that challenges to sorting Plato's dialogues by date, more general challenges to historicist interpretations of Plato's dialogues, as well as recent literary criticisms of Socratic studies all fail to undermine the research programme. We conclude with some thoughts about how and why Socratic studies has proved itself a valuable and fruitful research programme. (shrink)