The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Cet essai biographique sur Kierkegaard permet au lecteur de cheminer dans sa pensée au fil de ses oeuvres et de découvrir qu'elle se concentre autour de deux thèmes majeurs : l'amour et de la foi. Ils sont comme deux horizons qui reviennent constamment sous sa plume sous des éclairages les plus divers. Tout ce que Kierkegaard a écrit ne se rapporte pas directement à ces deux notions mais on peut risquer l'hypothèse que l'essentiel de ce qu'il a publié est une (...) longue méditation sur celles-ci. L'auteur présente aussi l'angoisse et le désespoir qui ont contribué à rendre le nom de Kierkegaard connu en dehors du monde des philosophes et des théologiens. Durant toute sa vie Kierkegaard a connu les veilleurs de nuit qui arpentaient les rues silencieuses de Copenhague. Le veilleur confortait le sommeil des habitants de la ville par son chant. Kierkegaard. au contraire, en choisissant le pseudonyme Vigilius Haufniensis espérait réveiller ses concitoyens à l'humain et à l'éthique chrétienne en déployant une activité littéraire presque surhumaine. À l'époque cependant, sa réussite fut limitée. Ce n'est qu'au XXe siècle que sa voix commença à être entendue dans son pays et ailleurs et aujourd'hui, presque deux cents ans après sa naissance, on peut légitimement penser qu'elle continue à surprendre et à déranger. (shrink)

En six occasions, Kierkegaard fut appelé à prendre la parole dans une église, mais n’ayant jamais été ordonné pasteur, il ne se considérait pas habilité à prêcher ni à intituler ses discours religieux prédications. Fidèle au culte dominical, sauf à la fin de sa vie, il portait une grande considération à la prédication et dans son œuvre protéiforme, on trouve de nombreuses réflexions sur la prédication en tant que catégorie, sur des prédications auxquelles il avait assisté et sur le rôle (...) du prédicateur. Quant à la prédication, sa tâche n’est pas de défendre le christianisme, mais de mettre en avant son caractère paradoxal lié au Christ comme source de scandale et modèle de l’existence chrétienne. Or parler de la prédication est aussi parler des prédicateurs. D’après Kierkegaard, le problème n’est pas leur orthodoxie dogmatique, mais l’adéquation entre leur existence et ce qu’ils prêchent. Théoriquement, n’importe qui peut donner une description objective de l’essence du christianisme, mais comment se conformer à la parole qui appelle à suivre le Christ outragé et rejeté? Celle-ci n’exige pas que les prédicateurs se transforment en martyrs ou en modèles de sainteté, sans tache ni ride, mais qu’ils avouent l’écart abyssal entre la radicalité de cette parole et leurs occupations ordinaires en tant que pères de famille, citoyens estimés, fonctionnaires de l’État. L’évêque Mynster, à la fois admiré et vitupéré, fut la figure emblématique de quelqu’un qui a annoncé un vrai christianisme, mais qui ne l’a pas vécu. Il lui a manqué ce que Kierkegaard appelle la réduplication. L’article se termine par une présentation des deux prédications que Kierkegaard prononça afin de passer l’épreuve homilétique en vue d’une éventuelle ordination pastorale. (shrink)

The doctrine of simple individuals has its equal and opposite reaction in the view that an individual is simply a bundle of properties, that the identity of an individual is entirely dependent on the identity of its properties. This view also seems to me to be in some sense wrong and I shall attack it in passing. If all my remarks have seemed excessively polemical it is because I have been anxious to make it as clear as possible what the (...) motivation behind this paper is. I am mainly concerned with the problem concerning the "it" which underlies or has properties and I shall want to argue that the identity of an individual--what it is that makes an individual that individual--does not depend merely on its being that individual or having that piece of substratum, but it depends partially and in a complicated way on the identity of its properties. The analysis will have to exhibit the nature of that dependence. Most of the discussion will revolve around proper names and their function since it is through linguistic considerations, I think, that we get the clearest illumination. The result, in case any one is interested, will be Absolute Idealism, or something like it. (shrink)

This popular choice for introductory philosophy courses again offers primary source readings woven into a text that is organized by key questions in philosophy. The discussion of each question is presented in a logical and historical light, showing connections, roots and influences. The clarity of the presentation and the successful student pedagogical aids provide an accessible, guided introduction to philosophy for college students.

A multidisciplinary faculty committee designed a curriculum to shape biomedical graduate students into researchers with a high commitment to professionalism and social responsibility and to provide students with tools to navigate complex, rapidly evolving academic and societal environments with a strong ethical commitment. The curriculum used problem-based learning (PBL), because it is active and learner-centred and focuses on skill and process development. Two courses were developed: Scientific Professionalism: Scientific Integrity addressed discipline-specific and broad professional norms and obligations for the ethical (...) practice of science and responsible conduct of research (RCR). Scientific Professionalism: Bioethics and Social Responsibility focused on current ethical and bioethical issues within the scientific profession, and implications of research for society. Each small-group session examined case scenarios that included: (1) learning objectives for professional norms and obligations; (2) key ethical issues and philosophies within each topic area; (3) one or more of the RCR instructional areas; and (4) at least one type of moral reflection. Cases emphasised professional standards, obligations and underlying philosophies for the ethical practice of science, competing interests of stakeholders and oversight of science (internal and external). To our knowledge, this is the first use of a longitudinal, multi-semester PBL course to teach scientific integrity and professionalism. Both faculty and students endorsed the active learning approach for these topics, in contrast to a compliance-based approach that emphasises learning rules and regulations. (shrink)

Objective We conducted a process evaluation to (a) assess the effectiveness of a new problem-based learning curriculum designed to teach professionalism and scientific integrity to biomedical graduate students and (b) modify the course to enhance its relevance and effectiveness. The content presented realistic cases and issues in the practice of science, to promote skill development and to acculturate students to professional norms of science. Method We used 5-step Likert-scaled questions, open-ended questions, and interviews of students and facilitators to assess curricular (...) effectiveness. Results Both facilitators and students perceived course objectives were achieved. For example, respondents preferred active learning over lectures; both faculty and students perceived that the curriculum increased their understanding of norms, role obligations and responsibilities of professional scientists. They also reported an increased ability to identify ethical situations and felt that they had developed skills in moral reasoning and effective group work. Conclusions These data helped to improve course implementation and instructional material. For example, to correct a negative perception that this was an ‘ethics’ course, we redesigned case debriefing activities to reinforce learning objectives and important skills. We refined cases to be more engaging and relevant for students, and gave facilitators more specific training and resources for each case. The problem-based learning small group strategy can stimulate an environment whereby participants are more aware of ethical implications of science, and increase their socialisation and open communication about professional behaviour. (shrink)

The title is an allusion to the fact that, traditionally, propositions have served at least two distinct functions in philosophy, even though these functions have not usually been distinguished. Propositions have been invoked as the ‘meanings’ or ‘intensions’ of sentences and as the objects of propositional attitudes. Thus the proposition that Socrates is wise is the meaning of the English sentence, ‘Socrates is wise,’ and is what Charles believes when he believes that Socrates is wise. ‘Means that’ and ‘believes that’ (...) take the same kind of object. I shall argue, first, that there are two quite different functions here and it takes two quite different kinds of proposition to serve these distinct functions. The second thing I want to do is examine the suggestion that we can treat propositions as sets of possible worlds. There is a serious difficulty here, and so I shall want to turn that idea on its side: I shall define possible worlds as sets of G-propositions and then define E-propositions as sets of possible worlds. (shrink)

Chapter I announces the aim of the book, which is, to deal with the question: What is a language? It also registers complaints against current semantical methods. The sections here are closely related to Quine's Two Dogmas, but the author finds himself dissatisfied, not just with analyticity, but also with logical truth, truth, designation. The difficulties are of two orders. In one case they would be dissolved by having general definitions of the terms in question. In the other case we (...) should have to discuss use of a language and that would take us into pragmatics. It turns out that to get our "general" definitions we have to define "language," "logical truth," and "G-designation" all at once, so to speak. Chapter II lays down criteria of adequacy for a definition of "language": two languages are identical if and only if they have the same vocabulary and every expression has the same significance in one language as it has in the other. Now the author has to cope with "significance." In Chapter III, he follows Quine in holding that an extensional languages recognizes at most individuals, truth-values, and classes; and an intensional or modal language recognizes at most individual concepts, properties, and propositions. The author wants to have it both ways: like lots of people, he wants individuals and properties and propositions. To have it both ways, he has to work out a new semantical method ; and since his properties and propositions are not the familiar intensions, he has to call them G-properties and G-propositions. If these entities are named in the language then they are G-designated by their names. (shrink)

I wish now to return to the elementary characterization of languagehood in section III and its rationalization in section IV and say something by way of conclusion. The account given may or may not have a large number of fascinating and important consequences, but I shall confine myself to a couple of minor points and one not so minor.Let us suppose that there are either an infinite number of extra-linguistic entities (which seems plausible) or an infinite number of possible expressions (...) (inscriptibles). Then, since the Descriptive Part of a language is just a finite mapping of expressions onto entities, there will be an infinite number of languages. The point is pretty obvious anyway. A language is presumably a linguistic structure (whatever that is) thatcould be used by intelligent creatures in exchanging information and in doing logic. There is no reason at all to suppose that the number of such structures is finite.The second minor point is derivative. There is no essential differencequa languages between the so-called natural languages and the so-called artificial languages. Consider hammers. Some hammers are actually used to drive nails. Some perish in warehouse fires before they ever have that honor. But all are equally hammers. It's the same with languages. Some are actually used, the vast majority, including the “artificial” languages defined in semantics books, are never used. But apart from differences in richness and complexity, all are equally languages.8But the major point I wished to bring out in this paper is the contrast between a language and its use, or, if you like, between a language and speech behaviour. I labored the distinction in my introductory remarks and in the body of the paper I offered a sketch of a purely semantical definition of ‘language’. Insofar as the apparatus goes any distance towards bringing order out of chaos then this circumstance vindicates the distinction. We say that Alexander is able to ride Bucephalus and is able to speak Greek. Just as in the first case we distinguish between what Alexander is able to do, namely ride Bucephalus, and what he is able to ride, namely, Bucephalus, so in the second we should distinguish between what Alexander is able todo, namely, speak Greek, and what he is able tospeak, namely, Greek. Strictly speaking, of course, we have to recognize the linguistician's commonplace distinction, within use, between the ability or competence to speak (use) a language and specific exercises of that ability, or performances9. This is the distinction between ‘He speaks English’ and ‘He is now speaking English’.Another example, closer to present concerns. We would have no trouble distinguishing between the ability to play the Bach Chaconne and performances of the Chaconne on the one hand, and on the other, the Chaconne itself; between what the violinist is able todo (viz., play the Chaconne) and what he is able to play (viz., the Chaconne). And once we accept the distinction we would expect to be able to describe the Chaconne —which is a sequence of sounds - independently of the behavior involved in playing it. An unedited score in fact does this. It is the violinteacher who talks about double stopping and so on.10 In the same way, it seems to me, if we accept the distinction between a language and its use we commit ourselves to discovering ways of giving a phonological-syntactical-semantical characterization of a languagewithout reference to behavior, without employing the word ‘uses’ - and this demand has exactly the same rationale as the demand that we keep psychology out of logic. Then in pure pragmatics, the word ‘uses’ comes into its own. (shrink)

We would like to thank an anonymous referee for his helpful comments on a previous version of this paper.

In lieu of an abstract, here is a brief excerpt of the content:Criminal Law, Pain Relief, and Physician Aid in DyingFaye Girsh, Ed.D., Executive DirectorMadam:The article by Cantor and Thomas on “Pain Relief, Acceleration of Death, and Criminal Law” (KIEJ, June 1996) was a tortured attempt to develop criteria for the humane and compassionate physician who tries to serve the needs of a patient in unremitting pain. There are three areas that merit comment.The authors dealt with pain medications that might (...) have the undesirable side effect of causing death. They did not mention tolerance, which usually occurs in a patient with chronic pain and which would require exceedingly high doses to be effective. They did not mention barbiturates, which are preferable to opiates in causing death and which are used increasingly by compassionate physicians to answer the pleas of their suffering patients, but for which there is no excuse about alleviating pain. Would the criminal law just call the prescription of a lethal dose of barbiturates a reckless act and require conviction? Fortunately, juries, as the authors point out, do not balance these formulas on the head of a pin. When they see the circumstances under which these doctors do help their patients, they choose to nullify the law and would ignore the suggestions made in this article.The authors refer to the “consent” of the patient. They do not mention that these doctors are operating with more than consent; they are administering these medications because suffering patients are begging them to put them out of their pain and the indignities of the dying process. The article discusses the process as though it were the same as consent to elective surgery. These patients—with AIDS, cancer, and hopeless neurological degeneration—are not simply agreeing to a procedure; they are desperately seeking a way out. If the criminal law were to develop criteria for physician aid in dying, certainly one of them should be the active, witnessed, repeated request of such a patient for a certain, quick, painless, gentle death.The third point is that physicians do not face prosecution when administering no treatment to a patient whose life could be saved with treatment but who chooses not to receive it. This has been upheld by the U.S. Supreme Court; no criteria for suffering, alternatives, terminality, justifiability, or unbearability are required. The doctor can stand by while the patient dies what may be a protracted, difficult death, but it is within the law. What matters in this situation is the decision of the patient to refuse treatment, and that is absolute. How ironic that the patient who cannot refuse treatment must, with his or her doctor, jump through all these hoops to achieve a peaceful death.One worries that the physician who must balance the risk of “risky pain relief” against the accusation of recklessness will err in the direction of allowing [End Page 103] the patient to bear the pain rather than help with a dose of analgesics that might be considered beyond the stipulated “risk.”Why don’t we just be honest about it? Allow dying or hopelessly ill patients to make the decision about what they want by passing a carefully defined law allowing euthanasia rather than balancing the risk and trying to determine the “purpose” of the physician’s ministrations. We protect some patients from themselves while allowing others almost complete autonomy to make the choice of ending their lives. The authors were right in saying that proponents of rational laws consider this sheer hypocrisy.Faye Girsh, Executive DirectorHemlock Society U.S.A. Denver, COFaye Girsh misconceives our article’s objective as an “attempt to develop criteria” for the humane physician. Our goal in writing the paper was to analyze the current criminal law framework in the hope of sharpening debate and engendering normative critiques. We readily acknowledge tensions in the current legal framework and would support changes in that framework.Copyright © 1997 The Johns Hopkins University Press... (shrink)

Reports from antiquity — two factual and another based on myth — claim that Ptolemy I was a son of the Macedonian king Philip II. If so, Ptolemy was a half-brother of Alexander the Great. Scholars suppose that this rumour was promoted by Ptolemy I. But this cannot be confirmed. It seems rather that Arsinoë, the mother of Ptolemy I, was a concubine at the court of Philip II and that a rumour existed that Ptolemy I was illegitimately born. This (...) rumour developed in two separate ways. In Macedon, probably in the late 280's BCE, it was claimed that the father of Ptolemy was Philip II. The story may have been inspired by Ptolemy Keraunos in the course of his quest for the Macedonian throne. In Egypt, however, in spite of an apparent reluctance of Ptolemy I to link Lagos with his name, it was officially proclaimed in the reign of his son that Lagos was the father of Ptolemy I. It is possible thereby that Ptolemy II removed the stigma of bastardy from the first Ptolemaic king. (shrink)