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)

Della Rocca concentrates on two problems crucial to Spinoza 's philosophy of mind: the requirements for having a thought about a particular object, and the problem of the mind's relation to the body. He contends that for Spinoza these two problems are linked and thus part of a systematic philosophy of mind.

Newly edited by Konrad Koerner (University of Ottawa), with an introduction by Clemens Knobloch (Universitat Siegen)The importance of Wegener's Untersuchungen uber die Grundfragen des Sprachlebens can only be compared to that of Karl Buhler's Sprachtheorie. Even now, however, Wegener's work remains virtually unknown to the English speaking world. Wegener's main work was published in 1885. It has its origin in two lectures given in 1883 and 1884 at school teacher meetings held in the Magdeburg area and it still recalls those (...) original occasions and maintains much of the oral style. Part of the volume treats the subject in a systematic and theoretical manner; other sections contain vivid examples and are characterized by a considerable didactic effort. The book is held together by leitmotif-questions, such as 'How do we understand language?' and 'How does language function as a means of everyday communication?'. We witness the experiences of the talented school teacher and the observations of the innovative dialect researcher combined, condensed, and conceptually ordered.In spite of the relatively unsystematic form of presentation, the book remains thoroughly consistent in thought and argument. In the Untersuchungen we have before us the outline of a communicative and functional view of language structure, of the analysis of speech, and of semantics. (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.

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 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 introduction of Linear Logic extends the Curry-Howard Isomorphism to intensional aspects of the typed functional programming. In particular, every formula of Linear Logic tells whether the term it is a type for, can be either erased/duplicated or not, during a computation. So, Linear Logic can be seen as a model of a computational environment with an explicit control about the management of resources.

The introduction of Linear Logic extends the Curry-Howard Isomorphism to intensional aspects of the typed functional programming. In particular, every formula of Linear Logic tells whether the term it is a type for, can be either erased/duplicated or not, during a computation. So, Linear Logic can be seen as a model of a computational environment with an explicit control about the management of resources.This paper introduces a typed functional language Λ! and a categorical model for it.The terms of Λ! encode (...) a version of natural deduction for Intuitionistic Linear Logic such that linear and non linear assumptions are managed multiplicatively and additively, respectively. Correspondingly, the terms of Λ! are built out of two disjoint sets of variables. Moreover, the λ-abstractions of Λ! bind variables and patterns. The use of two different kinds of variables and the patterns allow a very compact definition of the one-step operational semantics of Λ!, unlike all other extensions of Curry-Howard Isomorphism to Intuitionistic Linear Logic. The language Λ! is Church-Rosser and enjoys both Strong Normalizability and Subject Reduction.The categorical model induces operational equivalences like, for example, a set of extensional equivalences.The paper presents also an untyped version of Λ! and a type assignment for it, using formulas of Linear Logic as types. The type assignment inherits from Λ! all the good computational properties and enjoys also the Principal-Type Property. (shrink)

This paper presents an argument for the Principle of Sufficient Reason, the PSR, the principle according to which each thing that exists has an explanation. I begin with several widespread and extremely plausible arguments that I call explicability arguments in which a certain situation is rejected precisely because it would be arbitrary. Building on these plausible cases, I construct a series of explicability arguments that culminates in an explicability argument concerning existence itself. This argument amounts to the claim that the (...) PSR is true. The plausibility of the initial cases in the series provides the basis of an argument for the PSR, an argument that can be rebutted only by drawing a line between the plausible early cases in the series and the apparently unacceptable later cases. I argue that no principled reason for drawing this line has been found and that one cannot draw an unprincipled or arbitrary line without begging the question. The paper concludes that, therefore, this defense of the PSR remains unrebutted and that we have a powerful, new reason to embrace the PSR. (shrink)

This first extensive study of Spinoza's philosophy of mind concentrates on two problems crucial to the philosopher's thoughts on the matter: the requirements for having a thought about a particular object, and the problem of the mind's relation to the body. Della Rocca contends that Spinoza's positions are systematically connected with each other and with a principle at the heart of his metaphysical system: his denial of causal or explanatory relations between the mental and the physical. In this way, (...) Della Rocca's exploration of these two problems provides a new and illuminating perspective on Spinoza's philosophy as a system. (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)

This paper critically examines a prominent and perennial strategy—found in thinkers as diverse as Kant and Shamik Dasgupta—of simultaneously embracing the Principle of Sufficient Reason and also limiting it so as to avoid certain apparently negative consequences of an unrestricted PSR. I will argue that this strategy of taming the PSR faces significant challenges and may even be incoherent. And for my purposes, I will enlist a generally derided argument by Leibniz for the PSR which will help us to see (...) the connections between the PSR and a radical form of monism. (shrink)

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

I argue that the standard counterexamples to the identity of indiscernibles fail because they involve a commitment to a certain kind of primitive or brute identity that has certain very unpalatable consequences involving the possibility of objects of the same kind completely overlapping and sharing all the same proper parts. The only way to avoid these consequences is to reject brute identity and thus to accept the identity of indiscernibles. I also show how the rejection of the identity of indiscernibles (...) derives some of its support from its affinity with a Kripkean account of trans-world identity and theories of direct reference. (shrink)

This paper analyzes and evaluates Spinoza way of carrying out his naturalistic program in psychology. I begin by examining Spinoza’s general metaphysical doctrine according to which each thing strives to preserve itself. While this doctrine cannot be true in its unqualified form, it does receive some support from Spinoza’s views on the nature of complex individuals. I then explore the problematic way in which Spinoza applies the doctrine of self -preservation to human psychology. The paper goes on the investigate the (...) naturalistic character of Spinoza’s views on such topics as irrational action, prudence, altruism, mental causation and the nature and classification of affects. (shrink)

Spinoza's response to a certain radical form of scepticism has deep and surprising roots in his rationalist metaphysics. I argue that Spinoza's commitment to the Principle of Sufficient Reason leads to his naturalistic rejection of certain sharp, inexplicable bifurcations in reality such as the bifurcations that a Cartesian system posits between mind and body and between will and intellect. I show how Spinoza identies and rejects a similar bifurcation between the representational character of ideas or mental states and the epistemic (...) status of these ideas, a bifurcation to which Spinoza sees the radical sceptic committed. Spinoza's rejection of this bifurcation helps to explain some of his most cryptic statements concerning scepticism and also reveals a promising and highly metaphysical strategy for understanding and responding to scepticism. (shrink)

European Journal of Philosophy, Volume 30, Issue 2, Page 565-577, June 2022.

Au xviie siècle, la dévotion à l’Enfant Jésus connaît un essor sans précédent. Cette spiritualité de l’Enfance s’articule autour des notions d’anéantissement, d’abnégation et d’abandon à Dieu, avec des âmes soumises dans des corps maîtrisés. Les chrétiens doivent s’identifier au Christ enfant, vivre dans la pauvreté, le dénuement et la dépendance qui était celle de l’enfant dans la crèche. Les femmes n’ont guère de mal à se reconnaître dans ce divin Enfant décrit comme « petit », faible et dépendant. Mais, (...) une fois « abandonnées à Dieu », elles donnent – littéralement – corps à l’Enfant Jésus et prennent la parole en son nom. Ainsi, loin du silence du nourrisson, les femmes utilisent cette forme de dévotion comme un moyen d’expression et de reconnaissance sociale. (shrink)