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)

Shows that many of our understandings about scientific thought can be corrected once we realise just how unnatural science is. Quoting scientists from Aristotle to Einstein, the book argues that scientific ideas are, with rare exceptions, counter-intuitive and contrary to common sense.

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.

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)

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)

(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.

Second part of the translation into Spanish of David Lewis' "New Work for a Theory of Universals", corresponding to the last sections of the original paper. || Segunda parte de la traducción al español del trabajo de David Lewis "New Work for a Theory of Universals", correspondiente a últimas secciones del artículo original. Artículo original publicado en: Australasian Journal of Philosophy, Vol. 61, No. 4, Dec. 1983, pp. 343-377.

This paper explores Kant’s account of propositional content and its implications for the relationship between his notions of knowledge (Wissen) and cognition (Erkenntnis). While previous commentators commonly read Kant as holding a Fregean theory of propositional content, in this paper I argue that Kant’s theory of propositional content aligns more closely with Peter Hanks’ recent account. According to my reading, Kant holds that individual acts of judging are both ontologically and explanatorily prior to propositions or Kantian judgments (Urteil). Furthermore, on (...) my reading, acts of judging for Kant are acts of assertively predicating a property of an object rather than merely acts of neutral predication. This reading challenges the lately popular view that Kant’s notions of knowledge and cognition are not only distinct but also disjunct. I instead suggest that we should regard Kantian knowledge that requires cognitions as its grounds as a species of Kantian cognitions. (shrink)

Lewis Gordon presents the first detailed existential phenomenological investigation of antiblack racism as a form of Sartrean bad faith. Bad faith, the attitude in which human beings attempt to evade freedom and responsibility, is treated as a constant possibility of human existence. Antiblack racism, the attitude and practice that involve the construction of black people as fundamentally inferior and subhuman, is examined as an effort to evade the responsibilities of a human and humane world. Gordon argues that the concept (...) of bad faith militates against any human science that is built upon a theory of human nature and as such offers an analysis of antiblack racism that stands as a challenge to our ordinary assumptions of what it means to be human. (shrink)

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)

For 30 years, Quine, a dominant figure in logical theory and philosophy of logic, has combined insights in methodology, language, epistemology, and ontology, to blur the boundaries of speculative metaphysics and natural sciences. This revised text contains two new essays with replies from Quine.

Challenging the notion of theory as white and experience as black, Lewis Gordon here offers a philosophical portrait of the thought and life of the Martinican-turned-Algerian revolutionary psychiatrist and philosopher Frantz Fanon as an example of "living thought" against the legacies of colonialism and racism, and thereby shows the continued relevance and importance of his ideas.

Learn to think critically with the leading introduction to reasoning and argumentation. Highlights In clear, reader-friendly language, The Power of Critical Thinking provides an engaging introduction to argumentation, deductive and inductive reasoning, inferencing, and evaluating scientific theories New Critical Thinking and the Media boxes in each chapter apply the principles of critical thinking to the realms of media, advertising, and news New content on "fake news," the COVID-19 pandemic, and other important contemporary topics reflects the changing world in which today's (...) students must apply their critical thinking abilities New and updated exercises offer extensive opportunities for students to practise the skills through which they will become active, engaged critical thinkers Additional online resources-including a study guide and practice quizzes for students as well as an instructor's manual, a test bank, and PowerPoint slides for instructors-offer stimulating materials to enhance the learning and teaching experiences. About the Authors Chris MacDonald is an associate professor and chair of the Law and Business Department at the Ted Rogers School of Management, Toronto Metropolitan University. Lewis Vaughn is an independent scholar and author of several textbooks on philosophy, ethics, and critical thinking. (shrink)

Recently, the practice of deciding legal cases on purely statistical evidence has been widely criticised. Many feel uncomfortable with finding someone guilty on the basis of bare probabilities, even though the chance of error might be stupendously small. This is an important issue: with the rise of DNA profiling, courts are increasingly faced with purely statistical evidence. A prominent line of argument—endorsed by Blome-Tillmann 2017; Smith 2018; and Littlejohn 2018—rejects the use of such evidence by appealing to epistemic norms that (...) apply to individual inquirers. My aim in this paper is to rehabilitate purely statistical evidence by arguing that, given the broader aims of legal systems, there are scenarios in which relying on such evidence is appropriate. Along the way I explain why popular arguments appealing to individual epistemic norms to reject legal reliance on bare statistics are unconvincing, by showing that courts and individuals face different epistemic predicaments (in short, individuals can hedge when confronted with statistical evidence, whilst legal tribunals cannot). I also correct some misconceptions about legal practice that have found their way into the recent literature. (shrink)

This volume in the series celebrates the philosophy of American Donald Davidson, whose process covers different types of philosophy. Admired for developing a system based on his theory of mind and language, he considers two of his most central interests to be the concepts of truth and objectivity.

In this undergraduate textbook Lewis R. Gordon offers the first comprehensive treatment of Africana philosophy, beginning with the emergence of an Africana consciousness in the Afro-Arabic world of the Middle Ages. He argues that much of modern thought emerged out of early conflicts between Islam and Christianity that culminated in the expulsion of the Moors from the Iberian Peninsula, and from the subsequent expansion of racism, enslavement, and colonialism which in their turn stimulated reflections on reason, liberation, and the (...) meaning of being human. His book takes the student reader on a journey from Africa through Europe, North and South America, the Caribbean, and back to Africa, as he explores the challenges posed to our understanding of knowledge and freedom today, and the response to them which can be found within Africana philosophy. (shrink)

If I were asked to put forward an ethical principle which I considered to be especially certain, it would be that no one can be responsible, in the properly ethical sense, for the conduct of another. Responsibility belongs essentially to the individual. The implications of this principle are much more far-reaching than is evident at first, and reflection upon them may lead many to withdraw the assent which they might otherwise be very ready to accord to this view of responsibility. (...) But if the difficulties do appear to be insurmountable, and that, very certainly, does not seem to me to be the case, then the proper procedure will be, not to revert to the barbarous notion of collective or group responsibility, but to give up altogether the view that we are accountable in any distinctively moral sense. (shrink)