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.

Walter Benjamin's Antifascist Education is the first comprehensive analysis of educational themes across the entirety of the critical theorist's diverse writings. Starting with Benjamin's early reflections on teaching and learning, Tyson E. Lewis argues that the aesthetic and cultural forms to which Benjamin so often turned-namely, radio broadcasts, children's theatrical productions, collections, cityscapes, public cinemas, and word games-swell with educational potentialities. What emerges from Lewis's reading is a constellational curriculum composed of minor practices such as poor teaching, absentminded (...) learning, and nondurational studying. This curriculum carries political significance, offering an antidote to past and present forms of fascist manipulation, hardness, and coldness. Walter Benjamin's Antifascist Education is a testimony to Benjamin's belief that "everyone is an educator and everyone needs to be educated and everything is education.". (shrink)

Christianity teaches that whenever evil is done, God had ample warning. He could have prevented it, but He didn't. He could have stopped it midway, but He didn't. He could have rescued the victims of the evil, but - at least in many cases - He didn't. In short, God is an accessory before, during, and after the fact to countless evil deeds, great and small. An explanation is not far to seek. The obvious hypothesis is that the Christian God (...) is really some sort of devil. Maybe He is a devil as popularly conceived, driven' by malice. Or maybe He is unintelligibly capricious. Or maybe He is a fanatical artist who cares only for the aesthetic quality of creation - perhaps the abstract beauty of getting rich variety to emerge from a few simple laws, or perhaps the concrete drama of human life with all its diversity - and cares nothing for the good of the creatures whose lives are woven into His masterpiece. Oust as a tragedian has no business providing a happy end out of compassion for his characters.) But no; for Christianity also teaches that God is morally perfect and perfectly benevolent, and that He loves all of His creatures; and that these things are true in a sense not a million miles from the sense in which we attribute morality, benevolence, or love to one another. (shrink)

Inoperative Learning draws upon the movement towards a weak philosophy that is currently gaining ground in educational philosophy: this weak philosophy does not offer a set of solutions or guidelines for improving educational outcomes, but rather renders assumptions about the theory-practice coupling that is so popular in contemporary education inoperative. By arguing that such logic reduces education to merely instrumental ends, which can only be assessed in terms of predefined measurement tools, this book presents a challenge to contemporary notions of (...) education as learning. There are various forms of inoperative education that temporarily suspend the goal-directedness of learning. From the perspective of learning, the neutralization of progress, growth, and maturity would usually be seen as obstacles needing to be overcome on the path toward set goals. Yet Lewis argues that a serious investigation of inoperativity opens up possibilities that would be otherwise unavailable in a world fixated on the question of learning. In dialogue with philosophers (Agamben, Benjamin, and Esposito), as well as authors (Kafka and Walser), and qualitative researchers (Lather), Lewis turns our collective attention to what remains when concepts such as learning, child development, teacher effectivity, and personal growth are left idle. Inoperative Learning presents a radical rewriting of educational possibilities. It should therefore be of great interest to educational researchers and educational philosophers concerned with the question of alternative logics of education beyond learning. The book may also be of interest to educational policy specialists who are looking for new and innovative forms of critique and analysis. (shrink)

Enhanced by many innovative exercises, examples, and pedagogical features, The Power of Critical Thinking: Effective Reasoning About Ordinary and Extraordinary Claims, Second Edition, explores the essentials of critical reasoning, argumentation, logic, and argumentative essay writing while also incorporating material on important topics that most other texts leave out. Author Lewis Vaughn offers comprehensive treatments of core topics, including an introduction to claims and arguments, discussions of propositional and categorical logic, and full coverage of the basics of inductive reasoning. Building (...) on this solid foundation, he also delves into areas neglected by other texts, adding extensive material on "inference to the best explanation" and on scientific reasoning; a thorough look at the evaluation of evidence and credibility; and a chapter on the psychological and social factors that can impede critical thinking. Additional notable elements are a chapter on moral reasoning, advice on how to evaluate Internet sources, and guidelines for evaluating occult, paranormal, or supernatural claims. The Power of Critical Thinking, Second Edition, integrates many pedagogical features including hundreds of diverse exercises, examples, and illustrations; progressive, stand-alone writing modules; numerous text boxes; step-by-step guidelines for evaluating claims, arguments, and explanations; a glossary of important terms; and many reminders, summaries, and review notes throughout. The text is supplemented by a companion website at www.oup.com/us/criticalthinking (offering a student study guide and more), and an Instructor's Manual with Test Questions (available both in print and on a CD). This unique text features a modular structure that allows instructors to teach the chapters in almost any order. Written in a student-friendly style and enhanced by humor where appropriate, it is ideal for courses in critical thinking, introduction to logic, informal logic, argumentative writing, and introduction to argumentation. New to the Second Edition * Full-color throughout and an expanded art program (37 more photos and illustrations) * A new writing module--an annotated sample student paper--and five additional essays for analysis * A new section on evaluating news reports and advertising * Timely discussions of intelligent design and population (nonintervention) studies * Expanded coverage of experts and authors and reasons to doubt their reliability * More "Field Problems" and exercise questions * Chapter objectives and key terms with definitions for each chapter. (shrink)

If a guilty offender is justly sentenced to be punished and an innocent volunteer agrees to be punished instead, is that any reason to leave the offender unpunished? In the context of mundane criminal justice, we mostly think not. But in a religious context, some Christians do believe in penal substitution as a theory of the atonement. However, it is not just these Christians, but most of us, who are of two minds. If the punishment is an imprisonment or death, (...) we do not believe in penal substitution. But if it’s a fine, even a big fine, we mostly do. (shrink)

My office is in a medical building in suburban Washington, D.C. —in Bethesda, named for the Biblical healing pool. All of the offices of my building are occupied by medical specialists, representing the most sophisticated training in the application of the scientific method. Downstairs and of service to all of us is a pharmacy, looking for all the world like a research laboratory with its gleaming surface, meticulous cleanliness, micro-balances, records, reference books, and cash register. It is neatly stocked with (...) modern, physiologically-defined preparations of active, predictable drugs. Among the enzymes, hormones, antibiotics, and chemo therapeutics for neoplasm, are a few newly hatched, unfledged remedies, but most are dependable and thoroughly assayed. The intently busy, white-coated, unsentimental pharmacists serve a hard-headed group of practitioners and a neighborhood of upper-class, well-educated patients. It is disconcerting, then, to see the undersurface of this sophistication, the irrational shadows beneath the science. On the front counter of the pharmacy are displayed attractive colored advertisements and pleasantly seductive inducements to self-improvement through diet cults and foods, tranquilizers, energizers, protein supplements, happiness promisers, preparations to enhance sexuality, vitamins artfully combined, and many packeted stuffs of no rational or pretended use whatsoever. “Why,” I ask the gimlet-eyed pharmacist, “do you have this large display of ‘Il Wah Genuine Chinese Ginseng, the Miraculous Herb of Life’? Doesn't it violate your university training? Your integrity as a modernist?” “Oh,” says he, “ginseng makes you feel better! You have more energy. You can do more! Lots of athletes use it, and people who work too hard and feel exhausted. It's only $3.45 a package. The prescriptions you give me once in a while yield no profit, but I sell a lot of ginseng. I use it myself!” Bemused, I walk back to my office, wondering about the easy abandonment of rationality, and pull down a box of medicinals collected the year before at an open-air pharmacy in the riverside markets of Brazil. The box gives forth deliciously rich forest smells. The packets within contain barks, roots, seeds, all of purported medical value. Other packets have amulets, charms, and protectives. The colorful labels on some of the patent medicines invoke ancient saints and healers, and promise happiness, health, prosperity and power. The essential rationale for their use in indigenous medicine was illusive to me despite many conversations with indigenous healers, and many times I have gone through the hundreds of items trying to find the key to what Brazilian and North American people fundamentally want from a pharmacy. In both cultures, where does magic stop and science begin? Do shops in both countries vend talismans in the search for the enhanced life, and fetishes against death? How much of all drug use is ritual and inchoate expectation? How can we reduce the mystification and incrementally increase the rationality of our pharmacopeia? (shrink)

Background Studying global health problems requires international multidisciplinary teams. Such multidisciplinarity and multiculturalism create challenges in adhering to a set of ethical principles across different country contexts. Our group on health system responses to violence against women (VAW) included two universities in a European high-income country (HIC) and four universities in low-and middle-income countries (LMICs). This study aimed to investigate professional and policy perspectives on the types, causes of, and solutions to ethical challenges specific to the ethics approval stage of (...) the global research projects on health system responses to VAW. Methods We used the Network of Ethical Relationships model, framework method, and READ approach to analyse qualitative semi-structured interviews (n = 18) and policy documents (n = 27). In March-July 2021, we recruited a purposive sample of researchers and members of Research Ethics Committees (RECs) from the five partner countries. Interviewees signposted policies and guidelines on research ethics, including VAW. Results We developed three themes with eight subthemes summarising ethical challenges across three contextual factors. The global nature of the group contributed towards power and resource imbalance between HIC and LMICs and differing RECs’ rules. Location of the primary studies within health services highlighted differing rules between university RECs and health authorities. There were diverse conceptualisations of VAW and vulnerability of research participants between countries and limited methodological and topic expertise in some LMIC RECs. These factors threatened the timely delivery of studies and had a negative impact on researchers and their relationships with RECs and HIC funders. Most researchers felt frustrated and demotivated by the bureaucratised, uncoordinated, and lengthy approval process. Participants suggested redistributing power and resources between HICs and LMICs, involving LMIC representatives in developing funding agendas, better coordination between RECs and health authorities and capacity strengthening on ethics in VAW research. Conclusions The process of ethics approval for global research on health system responses to VAW should be more coordinated across partners, with equal power distribution between HICs and LMICs, researchers and RECs. While some of these objectives can be achieved through education for RECs and researchers, the power imbalance and differing rules should be addressed at the institutional, national, and international levels. Three of the authors were also research participants, which had potential to introduce bias into the findings. However, rigorous reflexivity practices mitigated against this. This insider perspective was also a strength, as it allowed us to access and contribute to more nuanced understandings to enhance the credibility of the findings. It also helped to mitigate against unequal power dynamics. (shrink)

CHAPTER The Excommunication of Baruch Spinoza The Decree of Anathema A man excommunicate is a man alone. He is severed from his past, his parents, teachers , ...

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)

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)

An account of Socrates' encounter with divine revelation.

Introduction: about philosophy in general and ethics in particular -- The good and bad in experience: prolegomena -- The good and bad in experience -- Semantics of the imperative -- Ethics and the logical -- Deliberate acts -- Right acts and good acts -- Right doing and the right to do -- We approach the normative finalities.

Learn to be responsible with Grover and your Sesame Street friends! Young readers will discover how to be a good helper to both themselves and those around them. Now in Spanish!

This third edition of Concise Guide to Critical Thinking covers all the fundamentals of critical thinking and does so as clearly and directly as possible.

Doing Ethics is the best-selling book for courses with an applied emphasis. It teaches moral decision making as an active process, giving students the theoretical and logical tools required to do ethics. The Fifth Edition offers expanded coverage of topics that students find relevant, including free speech on campus, hook-up culture, sexual consent, racism, and discrimination. A NEW InQuizitive adaptive learning tool features game-like activities that build mastery of core concepts and theories.

Writing Philosophy: A Student's Guide to Reading and Writing Philosophy Essays, Second Edition, is a concise, self-guided manual that covers how to read philosophy and the basics of argumentative essay writing. It encourages students to master fundamental skills quickly--with minimal instructor input--and provides step-by-step instructions for each phase of the writing process, from formulating a thesis, to creating an outline, to writing a final draft, supplementing this tutorial approach with model essays, outlines, introductions, and conclusions. Writing Philosophy is just $5 (...) when packaged with any Oxford University Press Philosophy text. Contact your Oxford representative for details and package ISBNs. (shrink)

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)

Première traduction française des écrits de mathématique et de philosophie, pleins d'humour, de l'auteur d'Alice au pays des merveilles, tirés de The Game of Logic, 1887, et de Symbolic Logic, 1896.Si l'on sait en général, que Lewis Carroll fut professeur de mathématiques, on sait plus rarement qu'il fut logicien, et ce avec passion.Sommaire : La logique et les mots dans l'œuvre de Lewis CarrollLa logique symboliqueA l'adresse des débutantsLes choses et leurs attributsLes propositionsLe diagramme bi-littéralLe diagramme tri-littéralLes syllogismesLa (...) méthode des indicesLes soritesProblèmes et solutionsA l'adresse des spécialistesQuelques sophismesCe que dirent Achille et la tortueLes trois coiffeursLewis Carroll logicien. (shrink)

Oswald Spengler was one of the most important thinkers of the Weimar Republic. In Oswald Spengler and the Politics of Decline, Ben Lewis completely transforms our understanding of Spengler by showing how well-connected this philosopher was and how, at every stage of his career, he attempted to intervene politically in the very real-life events unfolding around him. The volume explains Spengler's politics as the outcome of a dynamic interplay between his meta-historical considerations on world history on the one hand, (...) and the practical demands and considerations of Realpolitik on the other hand. (shrink)

The ethical philosophy of Emmanuel Levinas is typically associated with a punishing conception of responsibility rather than freedom. In this chapter, our aim is to explore Levinas’s often overlooked theory of freedom. Specifically, we compare Levinas’s account of freedom to the Kantian (and Fichtean) idea of freedom as autonomy and the Hegelian idea of freedom as relational. Based on these comparisons, we suggest that Levinas offers a distinctive conception of freedom—“finite freedom.” In contrast to Kantian autonomy, finite freedom constitutively involves (...) standing in certain social relations with others. And in contrast to Hegelian relational freedom, the social relations involved in finite freedom are not defined by mutual recognition, but by feelings of separation and even antagonism. Along the way, we promote a reading Levinas’s Totality and Infinity as a Hegel-style story of Bildung (development), and show how, on Levinas’s view, freedom can develop or mature in the life of the individual. (shrink)