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)

BackgroundPreprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An objective dimension of quality that is readily measurable is completeness of reporting, as transparency can improve the reader’s ability to independently interpret data and reproduce findings.MethodsIn this observational study, we initially compared independent samples of articles published in bioRxiv and in PubMed-indexed journals in 2016 using a quality of reporting questionnaire. After that, we performed paired comparisons (...) between preprints from bioRxiv to their own peer-reviewed versions in journals.ResultsPeer-reviewed articles had, on average, higher quality of reporting than preprints, although the difference was small, with absolute differences of 5.0% [95% CI 1.4, 8.6] and 4.7% [95% CI 2.4, 7.0] of reported items in the independent samples and paired sample comparison, respectively. There were larger differences favoring peer-reviewed articles in subjective ratings of how clearly titles and abstracts presented the main findings and how easy it was to locate relevant reporting information. Changes in reporting from preprints to peer-reviewed versions did not correlate with the impact factor of the publication venue or with the time lag from bioRxiv to journal publication.ConclusionsOur results suggest that, on average, publication in a peer-reviewed journal is associated with improvement in quality of reporting. They also show that quality of reporting in preprints in the life sciences is within a similar range as that of peer-reviewed articles, albeit slightly lower on average, supporting the idea that preprints should be considered valid scientific contributions. (shrink)

Insieme a John McDowell, Robert Brandom è uno dei filosofi emergenti della reazione al naturalismo filosofico; seguace Wilfrid Sellars, è l'autore americano che più si avvicina al dialogo con la filosofia continentale e propone una rivalutazione di Kant e Hegel nella filosofia analitica. Già allievo di Richard Rorty, Brandom è diventuo famoso con la pubblicazione di Making it Explicit. Questo ponderoso volume di 900 pagine non ha avuto però ancora una sufficiente attenzione nel dibattito filosofico italiano (a parte alcuni (...) inteventi pubblicati su Iride). Forse questo dipende in parte dalla peculiarità e difficoltà del suo approccio, in parte dalla mole stessa del citato volume. Anche per questo motivo Brandom ha presentato una serie di lezioni2 ove riprende i temi del libro maggiore e ne approfondisce alcune parti. In quanto segue si presentano i temi fondamentale di Making it Explicit, arricchiti con elementi presi dal nuovo approfondimento. (shrink)

Después de enseñar la asignatura de Ética, y de la aplicar unas normas familiares escolares tradicionales, los estudiantes no se apropian de elementos éticos por varias causas: no les ven utilidad, no comprenden el contexto, o simplemente no les afecta, anulando cualquier interés al respecto. Esto impide que su obrar en la cotidianidad no sea tolerante en su ambiente escolar, generando dificultades en el docente para mediar comportamientos opuestos a una cultura de paz. Ante esto, se propone la Filosofía para (...) Niños (FpN) como apuesta ético-política que permita robustecer el pensamiento crítico, creativo y cuidadoso para mirar hacia una cultura de paz. Diego Pineda, el fundador de FpN en Colombia, sostiene que es necesario desarrollar en los estudiantes habilidades de pensamiento que, adicionales a conocimientos éticos-ciudadanos, los lleve a tomar decisiones acertadas en el abordaje pacífico del conflicto. El desarrollo paulatino del pensamiento, la cercanía a las comunidades de indagación, la incursión en habilidades cognitivas y éticas producto de las herramientas pedagógicas propias del programa de FpN, constituyen una preparación para asumir posiciones argumentadas frente a dilemas que acontecen dentro de los conflictos escolares, ello facilitará al estudiante estructurarse y lograr tomar decisiones iluminadas por la razón. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:264 HISTORY OF PHILOSOPHY right at hand, without getting in the way. If it had been printed in as readable type and as elegant form as Steinmann's edition, it might be the ideal easily accessible version to familiarize us with the Pens~es as they were actually written and classified by Pascal himself. RICHARD H. POPKIN University of California, San Diego Pascal. Quinta edizione riveduta e aumentata. By Michele (...) Federico Sciacca. (Milano: Carlo Marzorati Editore, 1962. Pp. 250. 2000 L.) This Pascal by Sciacca consists of three parts. The first gives and considers the Life of Pascal (1623-1662) in connection with his complex and restless century (pp. 13--72). The second part (pp. 75-112) analyzes the relationship of Pascal with Jansenism. Pascal is both dependent on and independent of it. The Jansenists discussed while Pascal felt. Jansenism could not find a stable equilibrium between nature and grace which Jansenism either contrasted or confused while Pascal well distinguishes these two orders. They are for him heterogeneous but the lower order leads to the higher. Without God, man is misery and darkness. With God, man can do all things (p. 118). The third part (pp. 115-219) is entitled The Christian Philosopher. It shows that man is made for the infinite. The true call of humanity is religious (p. 206). The final conclusion is that Pascal can still teach us to exist (p. 216). PAUL Y. FUHRMANN Columbia Theological Seminary Louis Thomassin (1619-95), ~tude bio-bibliographique avec vingt lettres et deux textes in~dits. By Pierre Clair. (Vol. I of the series Le mouvement des idles au XVH" si~cle, Collection dirig~e par Andr~ Robinet.) (Paris: 1964. Pp. 160. NF 12.) This small volume is the first in a new series devoted to bringing to light various figures and aspects of seventeenth-century thought that have either been set aside, forgotten, or are only dimly known. Louis Thomassin (as well as Bernard Lamy who is the subject of the second volume that has appeared in this series) certainly falls in these categories. Although his name often turns up in discussions of Cartesianlsm, Jansenism, Malebranchism, etc., very little consideration is ever given to him as a fairly important personage of the time, or to his ideas and the role they played. This volume by Dr. Clair will be of much use to seventeenth-century scholars in providing the basic data about his life, his connections with several of the vital movements of the period, the fundamental bibliographical materials, as well as publishing two texts and twenty letters not before available. The biographical section (pp. 1-84) traces (a bit too episodically) Thomassin's education, his career among the Oratorians as a professor of humanities, philosophy, and theology, his possible involvements with the Jansenists, his difficulties as a result of his first published work, Dissertations sur les Conciles (1667) (suppressed the same year), his later successes for his many other works in theology, philosophy, history, and pedagogy, and his relations with various major and minor figures of the mid- and late seventeenth century, like Arnauld, Malebranche, Richard Simon, Bayle, Huet, etc. Section II (pp. 85-99) gives a detailed bibliography of Thomassin's published works, plus a list of his manuscripts located in various French libraries. This is followed by twenty letters of Thomassin, an intriguing and interesting discourse on the difference between history and science, and one on the nature of chronology, plus three letters by Thomassin's secretary, Nicolas Barat. In a brief BOOK REVIEWS 265 concluding chapter (pp. 150-52), Dr. Clair deals with "Comment lire l'oeuvre du P. Thomassin," providing much guidance to anyone who wishes to avail himself of the rich resources in Thomassin's writings. From the point of view of the history of philosophy, the most interesting aspects of Thomassin's thought seem to be (1) his "Cartesianism," that is, the extent to which he early imbibed Descartes' new ideas, and played a role in the fusion of the views of Augustine, B6rulle, and Descartes that developed in the Oratory, (2) his attempt to find a viable theory of the nature of Grace somewhere between Arnauld and Malebranche, and (3) his... (shrink)

Research in the discipline of international relations finds that the great democratic powers are less likely to pursue revisionist policies. This investigation challenges this argument by showing that the United States' decision to oust Saddam Hussein's regime in March 2003 was consistent with a modified version of John Mearsheimer's theory of offensive realism, which finds that great powers' motivation is global hegemony. This article is divided into three sections. The first section considers the value of Mearsheimer's theory and reworks it (...) by adding domestic variables to explain why states abandon defensive strategies for offensive ones. The second section shows how pre-9/11 American foreign policy strategy was, for the most part, status quo oriented, and section three explains why and how the Bush administration introduced a revisionist foreign policy strategy after the 9/11 attacks. This investigation concludes by showing how the 2003 Iraq War is the first step in the United States' quest for global hegemony. (shrink)

Emotionen haben als menschliches Phanomen schon fruh bei Philosophen und Dichtern grosses Interesse geweckt. Fur manche Denker waren sie nur negativ, andere dagegen sahen sie als unentbehrlicher Bestandteil der menschlichen Seele. Seit der Antike versucht man, die primaren Emotionen von abgeleiteten zu unterscheiden, um sie besser erforschen zu konnen. Jahrhundertelang galten Emotionen als der Vernunft entgegengesetzte, das logische Denken storende und aus den tiefsten und unreinsten Teilen der Seele hervortretende Krafte. Der Autor betrachtet verschiedene Theorien uber Emotionen sowohl aus einer (...) geschichtlichen als auch aus einer moderneren wissenschaftlichen Perspektive. Daruber hinaus versucht er, Emotionen nicht nur im Lichte theoretischer Uberlegungen zu sehen, sondern sie auch auf Grund seiner Erfahrungen als Arzt und Psychotherapeut zu verstehen. Dabei ruckt er die fur die Psyche wesentliche Wechselwirkung zwischen Denken und Fuhlen in den Vordergrund.". (shrink)

The ArgumentIt has long been apparent that in the nineteenth century, mathematics in France and England developed along different lines. The differences, which might well be labelled stylistic, are most easy to see on the foundational level. At first this may seem surprising because it is such a fundamental area, but, upon reflection, it is to be expected. Ultimately discussions about the foundations of mathematics turn on views about what mathematics is, and this is a question which is answered by (...) a variety of different groups including mathematicians, students, curricular planners, parents, etc. Mathematical practice rests on some kind of mixture of the answers to this fundamental question which come from these diverse groups. Comparing the cultural matrices which supported mathematics in France and Britain in the first decades of the nineteenth century sheds light on the real though often subtle differences in the ways the subject was pursued in the two countries. (shrink)

ArgumentThis paper traces the changing fortunes of natural theology in two generations of an English family. The group is represented in the first generation by the Unitarian radical, William Frend, and in the second by the spiritualist Sophia Frend De Morgan and her husband, the mathematician Augustus De Morgan. The Frend/DeMorgans were distinguished from the naturalistic Darwins by their commitment to reason; they were a quintessentially urban group whose impulses to natural theology flowed from a God they encountered through their (...) minds. For William Frend, natural theology was rooted in a tightly disciplined, linguistic view of reason that linked theological and mathematical understandings; in the De Morgan's generation, however, understandings of mathematics and of language changed in ways that undercut the power of Frend's reasoned approach. In its rise and fall this family story of reasoned theology is co-temporal with the natural theology that was wrecked on the rocks of Darwinian evolutionary theory. (shrink)