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)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

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)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (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)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

This book is a defense of modal realism; the thesis that our world is but one of a plurality of worlds, and that the individuals that inhabit our world are only a few out of all the inhabitants of all the worlds. Lewis argues that the philosophical utility of modal realism is a good reason for believing that it is true.

David Lewis (1941-2001) was Class of 1943 University Professor of Philosophy at Princeton University. His contributions spanned philosophical logic, philosophy of language, philosophy of mind, philosophy of science, metaphysics, and epistemology. In On the Plurality of Worlds, he defended his challenging metaphysical position, "modal realism." He was also the author of the books Convention, Counterfactuals, Parts of Classes, and several volumes of collected papers.

A lineage of prominent philosophers who have discussed the second-person relation can be regarded as advancing structural accounts. They posit that the second-person relation effects one transformative change to the structure of practical reasoning. In this paper, I criticise this orthodoxy and offer an alternative, substantive account. That is, I argue that entering into second-personal relations with others does indeed affect one's practical reasoning, but it does this not by altering the structure of one's agential thought, but by changing what (...) reasons can become available. The importance of second-personal thought for action is heterogenous. Second-person relations make possible the emergence of a wide variety of different kinds of practical reasons: creating some, revealing others. Recognising this diminishes the appeal of the traditional, structural accounts of the practical significance of such second-personal relations. Moving away from structural accounts facilitates a more thorough understanding of the intersubjective form of action. (shrink)

According to a recent paper by Tim Maudlin, Bell’s theorem has nothing to tell us about realism or the descriptive completeness of quantum mechanics. What it shows is that quantum mechanics is non-local, no more and no less. What I intend to do in this paper is to challenge Maudlin’s assertion about the import of Bell’s proof. There is much that I agree with in the paper; in particular, it does us the valuable service of demonstrating that Einstein’s objections to (...) quantum mechanics have nothing to do with its indeterminism. But I do think that Maudlin’s conclusion is overly cut-and-dried. Quantum mechanics is far from a unified edifice, and what Bell’s theorem shows depends on what version of quantum mechanics you look at. In particular, I’ll try to make the case that there’s an interesting, if ultimately uncompelling anti-realist construal of the import of Bell’s theorem. And I also want to suggest that locality isn’t quite as decisively defeated as Maudlin claims. (shrink)

(Citation/Reference) Williams, S. H. Lewis Carroll handbook.

(Statement of Responsibility) by Lewis Carroll ; with illustrations in colors.

The two works reprinted in this volume are a unique fusion of logical thought and inimitable whimsy. Written by the 19th-century mathematician who also gave us "Alive in Wonderland", they are among the most entertaining logical works ever written, and contain some of the most thought-provoking puzzles ever devised.

Many artists and music labels rely on partnerships with brands to pay for the production costs of their music videos. In exchange, the brands are featured in those videos. To enhance the transparency of these embedded forms of advertising, sponsorship disclosures are required. However, it remains unknown what the content of these disclosures in music videos should be to enhance sponsor transparency for adolescents. We examined how disclosure type affected adolescents’ conceptual and attitudinal persuasion knowledge. In addition, effects on responses (...) toward the brand, music video, and artist were examined. An experiment showed that none of the tested disclosures enhanced adolescents’ conceptual persuasion knowledge. However, disclosures explaining that the embedded brand helped pay for the production cost of the video led to lower attitudinal persuasion knowledge and, consequently, to more positive attitudes toward the brand, video, and artist, and to increased intentions to purchase the brand. (shrink)

Young single women's and men's cognitive scripts for the event “a first date” were examined to determine their content and to test for hypothesized differences in behavioral expectations. Participants were asked to list 20 expected actions involved in a first date for a woman and for a man. High agreement among participants was found for the content and sequence of actions that hypothetically would occur on a first date. The respondents listed a total of 19 different actions for women, and (...) 27 for men. The scripts for women and men differed significantly. The scripts for women emphasized the private sphere ; the scripts for men focused on control of the public domain. Gender roles were more prevalent in experienced daters' scripts. The results indicate that young adults' interpersonal scripts for dating maintain the traditional gender-power ratio. (shrink)

(Statement of Responsibility) by Lewis Carroll ; with ninety-two illustrations by John Tenniel.

Moral reasoning in bioethics -- Bioethics and moral theories -- Paternalism and patient autonomy -- Truth-telling and confidentiality -- Informed consent -- Human research -- Abortion -- Reproductive technology -- Genetic choices -- Euthanasia and physician assisted suicide -- Dividing up health care resources.

C. S. Lewis takes us on a profound journey through both heaven and hell in this engaging allegorical tale. Using his extraordinary descriptive powers, Lewis introduces us to supernatural beings who will change the way we think about good and evil.

C. S. Lewis sets out to persuade his audience of the importance and relevance of universal values such as courage and honor in contemporary society.

This comprehensive history of German philosophy from its medieval beginnings to near the end of the eighteenth century explores the spirit of German intellectual life and its distinctiveness from that of other countries. Beck devotes whole chapters to four great philosophers -- Nicholas of Cusa, Leibniz, Lessing, and Kant -- and extensively examines many others, including Albertus Magnus, Meister Eckhart, Paracelsus, Kepler, Mendelssohn, Wolff, and Herder. Questioning explanations of philosophy by the racial or ethnic character of its exponents, Beck's conclusion (...) is that German philosophy developed as a series of diverse responses to the historical experiences of the German people. The peculiarities of German philosophy must be viewed in the light of German political problems and educational structures. In particular he stresses the importance of the connections between philosophy and Germany's intellectual, literary, religious, and political history. (shrink)

Would you want to be operated on by a surgeon trained at a medical school that did not evaluate its students? Would you want to fly in a plane designed by people convinced that the laws of physics are socially constructed? Would you want to be tried by a legal system indifferent to the distinction between fact and fiction? These questions may seem absurd, but these are theories being seriously advanced by radical multiculturalists that force us to ask them. These (...) scholars assert that such concepts as truth and merit are inextricably racist and sexist, that reason and objectivity are merely sophisticated masks for ideological bias, and that reality itself is nothing more than a socially constructed mechanism for preserving the power of the ruling elite. In Beyond All Reason, liberal legal scholars Daniel A. Farber and Suzanna Sherry mount the first systematic critique of radical multiculturalism as a form of legal scholarship. Beginning with an incisive overview of the origins and basic tenets of radical multiculturalism, the authors critically examine the work of Derrick Bell, Catherine MacKinnon, Patricia Williams, and Richard Delgado, and explore the alarming implications of their theories. Farber and Sherry push these theories to their logical conclusions and show that radical multiculturalism is destructive of the very goals it wishes to affirm. If, for example, the concept of advancement based on merit is fraudulent, as the multiculturalists claim, the disproportionate success of Jews and Asians in our culture becomes difficult to explain without opening the door to age-old anti-Semitic and racist stereotypes. If historical and scientific truths are entirely relative social constructs, then Holocaust denial becomes merely a matter of perspective, and Creationism has as much "validity" as evolution. The authors go on to show that rather than promoting more dialogue, the radical multiculturalist preferences for legal storytelling and identity politics over reasoned argument produces an insular set of positions that resist open debate. Indeed, radical multiculturalists cannot critically examine each others' ideas without incurring vehement accusations of racism and sexism, much less engage in fruitful discussion with a mainstream that does not share their assumptions. Here again, Farber and Sherry show that the end result of such thinking is not freedom but a kind of totalitarianism where dissent cannot be tolerated and only the naked will to power remains to settle differences. Sharply written and brilliantly argued, this book is itself a model of the kind of clarity, civility, and dispassionate critical thinking which the authors seek to preserve from the attacks of the radical multiculturalists. With far-reaching implications for such issues as government control of hate speech and pornography, affirmative action, legal reform, and the fate of all minorities, Beyond All Reason is a provocative contribution to one of the most important controversies of our time. (shrink)

Blue collar women in declining industries tend to suffer permanent job loss as a result of dislocation, and women living in rural areas may be particularly vulnerable to extended unemployment. Relatively little is known about their experiences, in part because existing conceptual models do not adequately represent women's perspectives. In this study it is proposed that an ethic of care, as conceptualized by Carol Gilligan, shapes women's interpretations of the meaning of job dislocation. Gilligan's constructs are applied to a study (...) of middle aged women who were dislocated when an apparel manufacturing plant in their rural Southern community closed unexpectedly. The focus is on three moral dilemmas and the opportunities for growth that occurred as a result of the crisis, as women reconstructed the meaning of the experience. The potential contributions of the ethic of care perspective to other studies of job loss is discussed. (shrink)

This volume is devoted to Lewis's work in metaphysics and epistemology. Topics covered include properties, ontology, possibility, truthmaking, probability, the mind-body problem, vision, belief, and knowledge. The purpose of this collection, and the volumes that precede and follow it, is to disseminate more widely the work of an eminent and influential contemporary philosopher. The volume will serve as a useful work of reference for teachers and students of philosophy.

This anthology is a thorough introduction to classic literature for those who have not yet experienced these literary masterworks. For those who have known and loved these works in the past, this is an invitation to reunite with old friends in a fresh new format. From Shakespeare's finesse to Oscar Wilde's wit, this unique collection brings together works as diverse and influential as The Pilgrim's Progress and Othello. As an anthology that invites readers to immerse themselves in the masterpieces of (...) the literary giants, it is must-have addition to any library. (shrink)

When this work was first published in 1960, it immediately filled a void in Kantian scholarship.

Three of the papers included here have not previously appeared in English, and five have not been published at all.

This Is A New Release Of The Original 1897 Edition.

The intellectual history of the last quarter of this century has been marked by the growing influence of Africana thought--an area of philosophy that focuses on issues raised by the struggle over ideas in African cultures and their hybrid forms in Europe, the Americas, and the Caribbean. Existentia Africana is an engaging and highly readable introduction to the field of Africana philosophy and will help to define this rapidly growing field. Lewis R. Gordon clearly explains Africana existential thought to (...) a general audience, covering a wide range of both classic and contemporary thinkers--from Douglass and DuBois to Fanon, Davis and Zack. (shrink)

D. H. Hodgson has argued that among highly knowledgeable and rational act-Utilitarians there is no non-Circular reason to be truthful or to expect truthfulness from others; wherefore these utilitarians forfeit the benefits of communication. I reply that hodgson goes wrong by tacitly assuming that his utilitarians have no premises to reason from except those that hodgson lays down in specifying the example under consideration.

Augustine of Hippo strongly influenced western theology, but he has often been accused of over-emphasizing the unity of God to the detriment of the Trinity. In Augustine and the Trinity, Lewis Ayres offers a new treatment of this important figure, demonstrating how Augustine's writings offer one of the most sophisticated early theologies of the Trinity developed after the Council of Nicaea. Building on recent research, Ayres argues that Augustine was influenced by a wide variety of earlier Latin Christian traditions (...) which stressed the irreducibility of Father, Son and Spirit. Augustine combines these traditions with material from non-Christian Neoplatonists in a very personal synthesis. Ayres also argues that Augustine shaped a powerful account of Christian ascent toward understanding of, as well as participation in the divine life, one that begins in faith and models itself on Christ's humility. (shrink)

Hans Jonas (1903–1993) was one of the most important German-Jewish philosophers of the 20th century. A student of Martin Heidegger and close friend of Hannah Arendt, Jonas advanced the fields of phenomenology and practical ethics in ways that are just beginning to be appreciated in the English-speaking world. Drawing here on unpublished and newly translated material, Lewis Coyne brings together for the first time in English Jonas's philosophy of life, ethic of responsibility, political theory, philosophy of technology and bioethics. (...) -/- In Hans Jonas: Life, Technology and the Horizons of Responsibility, Coyne argues that the aim of Jonas's philosophy is to confront three critical issues inherent to modernity: nihilism, the ecological crisis and the transhumanist drive to biotechnologically enhance human beings. While these might at first appear disparate, for Jonas all follow from the materialist turn taken by Western thought from the 17th century onwards, and he therefore seeks to tackle all three issues at their collective point of origin. This book explores how Jonas develops a new categorical imperative of responsibility on the basis of an ontology that does justice to the purposefulness and dignity of life: to act in a way that does not compromise the future of humanity on earth. -/- Reflecting on this, as we face a potential future of ecological and societal collapse, Coyne forcefully demonstrates the urgency of Jonas's demand that humanity accept its newfound responsibility as the 'shepherd of beings'. (shrink)

How do we use our mental images of the present to reconstruct our past? Maurice Halbwachs addressed this question for the first time in his work on collective memory, which established him as a major figure in the history of sociology. This volume, the first comprehensive English-language translation of Halbwach's writings on the social construction of memory, fills a major gap in the literature on the sociology of knowledge. Halbwachs' primary thesis is that human memory can only function within a (...) collective context. Collective memory, Halbwachs asserts, is always selective; various groups of people have different collective memories, which in turn give rise to different modes of behavior. Halbwachs shows, for example, how pilgrims to the Holy Land over the centuries evoked very different images of the events of Jesus' life; how wealthy old families in France have a memory of the past that diverges sharply from that of the nouveaux riches; and how working class construction of reality differ from those of their middle-class counterparts. With a detailed introduction by Lewis A. Coser, this translation will be an indispensable source for new research in historical sociology and cultural memory. Lewis A. Coser is Distinguished Professor of Sociology Emeritus at the State University of New York and Adjunct Professor of Sociology at Boston College. (shrink)