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)

Provides a critical and analytical history of ancient Greek theories on the nature of pleasure, and of its value and rolein human lfie, from the ealriest times down to the period of Epicurus and the early Stoics.

Incompatibilism, the view that free will and determinism are incompatible, subsists on two widely accepted, but deeply confused, theses concerning possibility and causation: (1) in a deterministic universe, one can never truthfully utter the sentence "I could have done otherwise," and (2) in such universes, one can never really take credit for having caused an event, since in fact all events have been predetermined by conditions during the universe's birth. Throughout the free will.

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)

Socrates is one of the most important figures in the history of Western philosophy, but also one of the least known, since he wrote nothing himself, and is known to us only via the writings of others. This book examines the relation of these portrayals, especially Plato's, to the historical person, and also discusses the significance of Socrates' thought to the development of Western philosophy as we know it today.

Historically Wales has been regarded as a country with relatively low levels of school exclusion, particularly in comparison with England. This has been used as an indicator of Wales’ commitment to the UN Convention on the Rights of the Child, which foregrounds a rights-based agenda that would argue school exclusion is a consequence of broader socio-economic structures than individual actions. However, simple analyses may mask a different picture of school exclusions in Wales. In this article, we study more detailed information (...) on formal school exclusions by looking at ‘instances’ of school exclusion, which considers the frequency and length of formal school exclusions in Wales, and alongside recorded school absence. The article also demonstrates that the pupils ‘at risk’ of formal school exclusion varies by when they experience school exclusion during their educational lifecourse. The article concludes by highlighting that patterns of school exclusion are complex, and that interpretation of these patterns depends on what kind of measure of school exclusion is used. By publishing these results, the article hopes to persuade policymakers and practitioners to re-examine their processes of exclusion to ensure they are commensurate with the law and to prevent unnecessary school exclusions. (shrink)

This article follows Deleuze in investigating the ways in which the symptom as a form of representation can be collapsed into immanence. Exploring the symptoms of schizophrenia and autism, it examines what implications such a collapse may have for the production of the symptom in its double articulation as representation and immanent production. The argument follows Deleuze and Guattari in asserting that symptoms hold an implicit limit for the social forms that deploy them. Arguing that schizophrenia, as one such limit, (...) has been successfully appropriated and deferred by postmodern capitalism, it is proposed that the proliferating symptom cluster of autism may indicate a new form of limit and that ‘‘becoming autistic’’ thus may have potential as revolutionary practice. (shrink)

Incompatibilism, the view that free will and determinism are incompatible, subsists on two widely accepted, but deeply confused, theses concerning possibility and causation: (1) in a deterministic universe, one can never truthfully utter the sentence “I could have done otherwise,” and (2) in such universes, one can never really receive credit or blame for having caused an event, since in fact all events have been predetermined by conditions during the universe’s birth. Throughout the free will literature one finds variations on (...) these two themes, often intermixed in various ways. When Robert Nozick2 describes our longing for “originative value” he apparently has thesis (2) in mind, and thesis (1) may underlie his assertion that “we want it to be true that in that very same situation we could have done (significantly) otherwise.” John Austin, in a famous footnote, flirts with thesis (1). (shrink)

Konrad Cramer, in “ Reflections on the Logical Structure of a Kantian Moral Argument ”, argues that the Universal Law Formulation of the Categorical Imperative is best understood as providing us with an indirect method for determining the moral permissibility of acting on our maxims. He then goes on argue, however, that no interpretation of UL is consistent with Kant’s epistemic claim that we can easily discover what morality demands of us. In response I argue that Cramer relies on an (...) excessively demanding interpretation of Kant’s epistemic claim and that his indirect interpretation of UL rests on a problematic account how our maxims relate to the actions that we perform on their basis. I then turn to the question of the overall plausibility of UL, and stress the need to interpret it within the context of Kant’s overall moral system. (shrink)

We investigate expansions of Heyting algebras in possession of a unary term describing the filters that correspond to congruences. Hasimoto proved that Heyting algebras equipped with finitely many normal operators have such a term, generalising a standard construction on finite-type boolean algebras with operators. We utilise Hasimoto’s technique, extending the existence condition to a larger class of EHAs and some classes of double-Heyting algebras. Such a term allows us to characterise varieties with equationally definable principal congruences using a single equation. (...) Moreover, in the presence of a dual pseudocomplement operation, discriminator varieties are characterised by a pair of equations. We also prove that a variety of dually pseudocomplemented EHAs with a normal filter term is semisimple if and only if it is a discriminator variety. This generalises two known results, one by Kowalski and Kracht for finite-type varieties of BAOs, and the other by the present author for dually pseudocomplemented Heyting algebras without additional operations. (shrink)

We investigate expansions of Heyting algebras in possession of a unary term describing the filters that correspond to congruences. Hasimoto proved that Heyting algebras equipped with finitely many normal operators have such a term, generalising a standard construction on finite-type boolean algebras with operators. We utilise Hasimoto’s technique, extending the existence condition to a larger class of EHAs and some classes of double-Heyting algebras. Such a term allows us to characterise varieties with equationally definable principal congruences using a single equation. (...) Moreover, in the presence of a dual pseudocomplement operation, discriminator varieties are characterised by a pair of equations. We also prove that a variety of dually pseudocomplemented EHAs with a normal filter term is semisimple if and only if it is a discriminator variety. This generalises two known results, one by Kowalski and Kracht for finite-type varieties of BAOs, and the other by the present author for dually pseudocomplemented Heyting algebras without additional operations. (shrink)

This first volume in the series traces the development of philosophy over two-and-a-half centuries, from Thales at the beginning of the sixth century BC to the death of Plato in 347 BC.

This chapter, which concentrates on the violent imaginaries that informed the reports and deeds of the 1994 Rwandan genocide, reviews the perseverance of pre-colonial notions of a sacred king whose “wild sovereignty” and inability to promote the flow of imaana earns him fateful sacrifice. The term imaana denotes a supreme being and, in a more generalized way, a “diffuse, fecundating fluid” of celestial origin whose activity upon livestock, land, and people brought fertility and abundance. As imaana's earthly representative, the king (...) channeled fertility to the rest of humanity. The chapter also discusses symbolism of the sovereign's body and its implicit link with the process of liquid flow. Habyarimana is an inadequate conduit of imaana and thus not a worthy king. He is the antithesis of Ruganzu Ndori. -/- . (shrink)

The question of concentration, or to use a word more in tune with the true nature of this essay, the heart, of this work is to explore the constructs surrounding the very nature and essence of the human heart. By heart I mean not the organ of flesh and blood, or the muscle that pumps life through out our corporal beings. But rather I mean to speak of an emotion that exists in parallel to the spirit or soul of the (...) human cognitive existence. I have chosen the title of this essay for a very specific reason, being that love and the human heart are two different concepts that I find to be closely related and essential for the other to exist. However, I findthat they are different and should be treated as such, for this reason I have given this essay a two-fold thesis. In that its main function will be to incorporate the idea of love with the ideologies of the human heart but also that they should be discussed separately. To most accurately address these points there will be three sections to this essay; the first will be an address on love and its meaning and purpose, the second will be in regards to the mystics of the heart, while the third will be a link between the two and act as a bridge from the psychological emotions of love to the physical and real emotions of man. (shrink)

Volume 1 of the _Routledge History of Philosophy_ covers one of the most remarkable periods in human thought. In the space of two and a half centuries, philosophy developed from quasi-mythological speculation to a state in which many of the most fundamental questions about the universe, the mind and human conduct had been vigorously pursued, and some of the most enduring masterworks of Western thought had been written. The essays present the fundamental approaches and thinkers of Greek philosophy in chronological (...) order. Each is written by a recognised authority in the particular field, and takes account of the large amount of high-quality work done in the last few decades on Platonic and pre-Platonic philosophy. All write in an accessible style, meeting the needs of the non-specialist without loss of scholarly precision. Topics covered range from early Greek speculative thought, its cultural and social setting, to the Sophists, Socrates and culminate in three chapters on Plato's lasting contribution to all central areas of philosophy. Supplemented with a chronology, a glossary of technical terms and an extensive bibliography, this volume will prove an invaluable and comprehensive guide to the beginnings of philosophy. (shrink)

Socrates has a unique position in the history of philosophy. His influence on Plato is credited with the development of Western philosophy. In this book Christopher Taylor explores the relationship between the historical Socrates and the Platonic character--and examines the enduring image of Socrates as the ideal exemplar of the philosophic life.

The theme of the third annual Spring workshop of the HUPO-PSI was proteomics and beyond and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups working on the similar issues of developing interchange standards and minimal reporting requirements. Significant developments in many of the HUPO-PSI XML interchange formats, minimal reporting requirements and accompanying controlled vocabularies were reported, with many of these now feeding into the broader efforts of the Functional Genomics Experiment data (...) model and Functional Genomics Ontology ontologies. (shrink)