The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

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)

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)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

Gregory Rocca's nuanced discussion prevents Aquinas's thought from being capsulized in familiar slogans and is an antidote to unilateralist or monochrome views about God-talk.

Until recently, Spinoza's standing in Anglophone studies of philosophy has been relatively low and has only seemed to confirm Friedrich Heinrich Jacobi's assessment of him as "a dead dog." However, an exuberant outburst of excellent scholarship on Spinoza has of late come to dominate work on early modern philosophy. This resurgence is due in no small part to the recent revival of metaphysics in contemporary philosophy and to the increased appreciation of Spinoza's role as an unorthodox, pivotal figure - indeed, (...) perhaps the pivotal figure - in the development of Enlightenment thinking. Spinoza's penetrating articulation of his extreme rationalism makes him a demanding philosopher who offers deep and prescient challenges to all subsequent, inevitably less radical approaches to philosophy. While the twenty-six essays in this volume - by many of the world's leading Spinoza specialists - grapple directly with Spinoza's most important arguments, these essays also seek to identify and explain Spinoza's debts to previous philosophy, his influence on later philosophers, and his significance for contemporary philosophy and for us. (shrink)

Escribir sobre ética —y en particular sobre ética médica— en los tiempos que corren comporta un cierto riesgo, no sólo por la posible incompetencia del autor, sino porque éste se encuentra algo desubicado en un entorno de crisis moral propiciada por el cientifismo como nueva religión laica y la voracidad de los mercados. La preocupación de los legos por la creciente dificultad en discernir aquello que es ético o bueno de lo que no lo es constituye en la actualidad un (...) dilema universal, al menos por cuanto respecta a nuestra civilización occidental. Dicha preocupación se encuentra plasmada en decenas de textos dedicados no ya a los aspectos más abstractos o filosóficos de la ética general, sino a las “éticas particulares” aplicables a las profesiones, las empresas o al ámbito político. Así, se habla de una ética periodística, del compliance industrial, de la investigación, de la banca, de las redes de sociales y, por supuesto de la medicina. (shrink)

The aim of this paper is to shed light on and develop what I call a phenomenological conception of experiential justification. According to this phenomenological conception, certain experiences gain their justificatory force from their distinctive phenomenology. Such an approach closely connects epistemology and philosophy of mind and has recently been proposed by several authors, most notably by Elijah Chudnoff, Ole Koksvik, and James Pryor. At the present time, however, there is no work that contrasts these different versions of PCEJ. This (...) paper not only bridges this gap, but also reveals problems in current versions of PCEJ. Consequently, I argue for a new version of PCEJ that focuses on what is given within experience and not on how what is given pushes me towards believing something. (shrink)

This paper offers a defense of a much-maligned Leibnizian argument for the Principle of Sufficient Reason, the principle according to which whatever is has a sufficient reason or explanation. While Leibniz’s argument is widely thought to rely on a question-begging premise, the paper offers a wholly original and non-question-begging defense of that premise, a defense that Leibniz did not anticipate. The paper does not present this defense of Leibniz's argument as an interpretation of Leibniz; rather, the paper—more modestly in one (...) way, less modestly in another—simply claims that this argument succeeds. (shrink)

In some developed nations, corporations are today legally regarded as “people”. But if that were literally true of the Weyland‐Yutani Corporation in the Alien franchise, the least it would deserve is a swift left‐hook to the jaw from Ripley and the few unfortunate persons who survive with her in each of the movies. The question of what constitutes good business practices is what business ethics is all about. In Alien, Carter Burke is the quintessential corporate weasel, and in many ways (...) it's almost as if Gordon Gekko was transported into science fiction. The problem of deferring accountability is unavoidable in any large company, and Weyland‐Yutani is no exception. There are two major approaches to ethics that can help us to understand the extent to which cost‐benefit reasoning is ethical. The first, defended and popularized by Immanuel Kant, is deontology. The second major approach to ethics is utilitarianism, whose most famous early proponent was John Stuart Mill. (shrink)

Supuestos y conceptos fundamentales del pensamiento juridico de san Agustin.--La idea del estado en san Agustin.

The Parmenidean Ascent is a full-throated and wide-ranging defense of an extreme form of monism or the denial of all distinctions, a form of monism rarely seen since the time of the pre-Socratic philosopher, Parmenides. At once historically sensitive and deeply engaged with trends in recent and contemporary metaphysics, philosophy of action, epistemology, and philosophy of language, The Parmenidean Ascent aims, on rationalist grounds and in a skeptical spirit, to challenge the content of-and to overturn the methods of much of (...) contemporary philosophy. (shrink)

The aim of this paper is twofold. The first is an interpretative one as I wish to provide a detailed account of Husserl’s conception of experiential justification. Here Ideas I and Introduction to Logic and Theory of Knowledge: Lectures 1906/07 will be my main resources. My second aim is to demonstrate the currency and relevance of Husserl’s conception. This means two things: Firstly, I will show that in current debates in analytic epistemology there is a movement sharing with Husserl the (...) basic idea that certain experiences gain their justificatory force simply from their distinctive phenomenal character. Secondly, I shall reveal the benefits of Husserl’s specific version of this view. Thus, one of my aims is to show that debates in current analytic epistemology could profit from adopting certain Husserlian elements. More precisely, I will defend Husserl’s claim that perceptual experiences are justifiers due to their self-giving phenomenal character as opposed to the currently popular view that it is the phenomenology of pushiness that makes them justifiers. To put it differently, what matters is what is originally given within experience and not how you feel about what is given. (shrink)

Reunindo o contributo de autores oriundos de múltiplas áreas, incidindo sobre a filosofia, as tradições religiosas e sapienciais, a história, a literatura, a linguística, a literatura oral, a obra que agora se publica, sob a égide do Centro de Estudos Clássicos e do Centro de Estudos Comparatistas da Faculdade de Letras da Universidade de Lisboa, constitui uma visão plural sobre a sabedoria, sobre o lugar da memória na compreensão sábia da realidade, enfim, sobre o modo como a sabedoria e a (...) memória se cruzam. (shrink)