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)

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)

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)

The path of those who would approach the study of Bentham's writings on Evidence has been considerably smoothed by the recent publication of William Twining's work on the evidence theories of Bentham and Wigmore. The material on evidence is now being tackled by the Bentham Project. It presents no easy task. The central core, The Rationale of Judicial Evidence, edited and published by John Stuart Mill in 1827, exists only in the printed version, the MSS from which Mill worked having (...) disappeared. But a substantial body of related material which survives has yet to be thoroughly investigated, though William Twining has made a gallant start. A new edition of the work hitherto known as ‘An Introductory View of the Rationale of Evidence’, first printed in full in the Bowring edition of the Works of Jeremy Bentham is in preparation. The first fruits of this endeavour is that the title of that work as it should appear in due course in the new Collected Works will be Introduction to the Rationale of Evidence: An Introductory View for the Use of Lawyers as well as Non-lawyers, the title in fact given to the work by Bentham. It is intended that what follows should similarly be of use to non-lawyers as well as lawyers. (shrink)

In this paper, we pose a speculative encounter between Heidegger and the Chinese Song Dynasty landscape painter Xia Gui. Our intention is to reassess Heidegger’s theory of the fourfold. By placing the concept in a cross-cultural context, we argue that Heidegger was essentially correct in that the world is structured as a fold between interrelated elements. At the same time, we challenge the quantity and quality of the folded elements. If one turns to the work of Xia Gui in conjunction (...) with relevant Daoist texts, what one finds is a threefold structure to the world, composed of earth, sky, and mortals without Heidegger’s emphasis on divinities. In conclusion, we suggest that studying the folding structure of the world ought to be done through cultural comparisons of philosophical and aesthetic traditions in order to understand the potentiality for worldhood as an xfold. (shrink)

For the first time, Walter Benjamin's critical comments on educator and philosopher Rudolf Steiner are examined in depth. In particular, Benjamin detected protofascist themes within Steiner's seemingly progressive notion of child-centered, arts-based, developmentally appropriate early childhood education. But this does not mean that Benjamin completely rejected Steiner's work as mere ideology. Instead, we can find the subtle trace of Steiner's influence in Benjamin's own reflections on childhood. Here Tyson E. Lewis calls for a dialectical approach modeled by Benjamin that (...) allows us to critically interrogate Steiner's progressive education for protofascist tendencies, while also redeeming various insights into the lives of children. This dialectical approach to understanding the complex relationship between progressive education and fascism is now more urgent than ever before. (shrink)

This study compares the relationship between the moral reasoning modes and leadership orientation of males versus females, and managers versus engineers/scientists. A questionnaire developed by Worthley (1987) was used to measure the degree of each participant's respective independence and justice, and relationships and caring moral reasoning modes. Leadership orientation values and attitudes were measured using the Fiedler and Chemers (1984) Least Preferred Coworker Scale.The results suggest that, although males differ from female in their dominant moral reasoning modes, managers are not (...) distinguishable from the engineers/scientists they manage in terms of their moral reasoning mode or Least Preferred Coworker score. (shrink)

This paper articulates the separate accounts of facial education and lecturing found in A Thousand Plateaus in order to theorize a new concept of lecturing for a post-digital university. Many accounts of Deleuze and Guattari in educational theory turn away from lecturing as hierarchical and striated, yet this approach denies Deleuze and Guattari’s deterritorialization of the practice through their description of a lecture by the character Professor Challenger. When read alongside their plateau on facialization, Challenger’s unusual performance can be interpreted (...) as an interruption of the abstract machine of facialization that animates traditional accounts of lecturing. The article concludes with implications for a de-faced form of lecturing for a post-digital university. (shrink)

Law and History contains a collection of essays by prominent legal historians, which explore the ways in which history has been used by lawyers past and present to answer legal questions. In common with earlier volumes in the Current Legal Issues series, it seeks both a theoretical and methodological focus. This volume covers a broad range of topics, from a discussion of the nature of norms in the middle ages to the role of war crimes trials in the twentieth century. (...) It includes wide-ranging historiographical discussions, which examine the nature and aims of the legal historian, as well as contributions which explore the methodology and aims of writers such as Coke, Maine, Weber, Montesquieu, and Kames, who sought to use historical models to explain law. A number of contributions examine developments in legal doctrine, particularly in the nineteenth century, including developments in the law of contract, administrative law, and perjury. These raise important questions about the nature of the legal categorizations which developed in that era. Law and History also includes a collection of contributons on the use of history in twentieth century trials, including the Nuremberg trials, the trial of the Gang of Four, and trials arising from the events in the former Yugoslavia and Rwanda. (shrink)

In this article, we explore the possibilities that works of art might possess for looking in original and unforeseen ways into something that, at first sight, has little to do with arts and artistic practice. To be more precise, we present here three artistic representations, taken from various times and style periods, that depict a well-known figure in art history: angels. A detailed description and analysis of these images give us the opportunity to figure out something about another figure, which (...) is fascinating to us as philosophers of education: the teacher. Our basic intuition is that the way in which three important artists—Albrecht Dürer, William Hogarth, and Paul Klee—have tried to capture and trace out... (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)

We show that in the c.e. weak truth table degrees if b < c then there is an a which contains no hypersimple set and b < a < c. We also show that for every w < c in the c.e. wtt degrees such that w is hypersimple, there is a hypersimple a such that w < a < c. On the other hand, we know that there are intervals which contain no hypersimple set.

The Oxford Handbook of Religious Conversion offers a comprehensive exploration of the dynamics of religious conversion, which for centuries has profoundly shaped societies, cultures, and individuals throughout the world. Scholars from a wide array of religions and disciplines interpret both the varieties of conversion experiences and the processes that inform this personal and communal phenomenon.This volume examines the experiences of individuals and communities who change religions, those who experience an intensification of their religion of origin, and those who encounter new (...) religions through colonial intrusion, missionary work, and charismatic and revitalization movements. The thirty-two innovative essays provide overviews of the history of particular religions, including Hinduism, Buddhism, Confucianism, Taoism, Sikhism, Islam, Christianity, Judaism, indigenous religions, and new religious movements. The essays also offer a wide range of disciplinary perspectives-psychological, sociological, anthropological, legal, political, feminist, and geographical-on methods and theories deployed in understanding conversion, and insight into various forms of deconversion. (shrink)

In an educational landscape dominated by discourses and practices of learning, standardized testing, and the pressure to succeed, what space and time remain for studying? In this book, Tyson E. Lewis argues that studying is a distinctive educational experience with its own temporal, spatial, methodological, aesthetic, and phenomenological dimensions. Unlike learning, which presents the actualization of a student’s "potential" in recognizable and measurable forms, study emphasizes the experience of potentiality, freed from predetermined outcomes. Studying suspends and interrupts the conventional (...) logic of learning, opening up a new space and time for educational freedom to emerge. Drawing upon the work of Italian philosopher and critical theorist Giorgio Agamben, Lewis provides a conceptually and poetically rich account of the interconnections between potentiality, freedom, and study. Through a mixture of educational critique, phenomenological description, and ontological analysis, Lewis redeems study as an invaluable and urgent educational experience that provides alternatives to the economization of education and the cooptation of potentiality in the name of efficiency. The resulting discussion uncovers multiple forms of study in a variety of unexpected places: from the political poetry of Adrienne Rich, to tinkering classrooms, to abandoned manifestos, and, finally, to Occupy Wall Street. By reconnecting education with potentiality this book provides an educational philosophy that undermines the logic of learning and assessment, and turns our attention to the interminable paradoxes of studying. The book will be key reading for scholars in the fields of educational philosophy, critical pedagogy, foundations of education, composition and rhetoric, and critical thinking and literacy studies. (shrink)