Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (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)

Der Laureatus dieser Schrift hatte 1986 Hans Jonas eröffnet, daß er an einer Politischen Philosophie arbeite, aus der, wie die Autoren dieses Bandes wissen, nichts geworden ist und von der man auch sonst nicht viel vernommen hat. Jonas wandte damals ein: "Wie wollen Sie der Politischen Vernunft auf die Beine helfen? Das Wissen über die politischen Bewußtseinsvoraussetzungen in uns und ihre Struktur in Gesellschaften ist in esoterische Teilbestände und exoterische politische Religionen, Ideologien und Denkschulen zerfallen. Diese Angelegenheit müßte einer umfassenden (...) Kritik unterzogen werden. Außerdem müßten alle gescheiterten Restitutionsversuche von Platon bis heute auf ihre Prägnanz hin durchgegangen werden. Er nannte Thomas von Aquin, Spinoza, Kant, Hegel, Arendt, Strauss, Voegelin und sich selbst. Sie müßten die Erfahrungen und die Maßstäbe, aus denen das politische Bewußtsein sich ernährt und aufrichtet und die, die es vergiften, frei legen." Im nachfolgenden Gespräch über verschiedene Denker und ihre Texte zur politischen Philosophie tauchten metaphorisch die "leuchtenden Fünkchen" oder "Goldklümpchen" auf, in denen Jonas und der Laureatus lebendige Reste der Politischen Vernunft und die menschheitliche Erinnerung an sie erkannten. "Wir sind womöglich aus einer Jeremiade herausgekommen …" lautete der verheißungsvolle Schlußpunkt des kurzen Gesprächs. Der Laureatus, Jurist und Politikwissenschaftler, konnte während seiner Lehr- und Forschungstätigkeit einige Anregungen für "philosophische Fragestellungen" zu den grotesken und verflachten Formationen des politischen Denkens unserer Zeit geben. Die Autoren sind Claus-Ekkehard Bärsch, Giandomenico Bonanni, Ulrich Diehl, Michael Ensslen, Jürgen Gebhardt, Volker Gerhardt, Manfred Henningsen, Vittorio Hösle, Klaus Kodalle, Peter König, Daniel Krochmalnik, Jan-Ivar Lindén, Reiner Manstetten, Krzysztof Maurin, Peter J. Opitz, Thomas Petersen, Walter Rothholz, Florian Sattler, Stephan Sattler, Julius H. Schoeps, Peter von Sivers, Chiara Staude-Colli, Jakob Staude, Kurt Stenzel, Peter Weber-Schäfer, Reiner Wiehl und James Wood. (shrink)

The 10th International Conference on Biomedical Ontology (ICBO 2019), was held at the Jacobs School of Medicine and Biomedical Sciences of the University at Buffalo, in Buffalo, NY, USA. It was the 10-year anniversary of the ICBO series, and the return of the conference to Buffalo after the first two ICBO conferences were held in Buffalo in 2009 and 2011. ICBO 2019 was well attended, with 115 registered attendees and additional walk-ins from the local academic community. The program included excellent (...) keynote talks by Barry Smith, “International Standard Ontology,” and Bjoern Peters, “Putting principles into practice: OBO ontologies and applications in immunology,” as well as 23 oral presentations, 26 posters, and one software presentation. There were 53 papers and abstracts submitted for peer-review to ICBO 2019. Each submission was reviewed by three members chosen from the Program Committee. Of these submissions, 43 were accepted for this volume: 19 full papers, 23 poster abstracts, and 1 software demonstration extended abstract. We thank our program committee for their thoughtful reviews. There were also three workshops and four tutorials (listed below) held in conjunction with the main ICBO 2019 meeting. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Der Mensch als Übender, als sich durch Übungen selbst erzeugendes Wesen - Rainer Maria Rilke hat den Antrieb zu solchen Exerzitien zu Beginn des 20. Jahrhunderts in die Form gefaßt: "Du mußt dein Leben ändern." In seinem Plädoyer für die Ausweitung der Übungszone des einzelnen wie der Gesellschaft entwirft Peter Sloterdijk eine grundlegende und grundlegend neue Anthropologie. Den Kern seiner Wissenschaft vom Menschen bildet die Einsicht von der Selbstbildung alles Humanen. Seine Aktivitäten wirken unablässig auf ihn zurück: die Arbeit (...) auf den Arbeiter, die Kommunikation auf den Kommunizierenden, die Gefühle auf den Fühlenden. Es sind die ausdrücklich übenden Menschen, die diese Existenzweise am deutlichsten verkörpern: Bauern, Arbeiter, Krieger, Schreiber, Yogi, Rhetoren, Instrumentalvirtuosen oder Models. Ihre Trainingspläne und Höchstleistungen versammelt dieses Buch zu einer vergnüglich-instruktiven Lektüre von den Übungen, die erforderlich sind, ein Mensch zu sein. (shrink)

Many technology ethicists hold that the time has come to articulate _neurorights_: our normative claims vis-à-vis our brains and minds. One such claim is the right to _mental integrity_ (‘MI’). I begin by considering some paradigmatic threats to MI (§1) and how the dominant autonomy-based conception (‘ABC’) of MI attempts to make sense of them (§2). I next consider the objection that the ABC is _overbroad_ in its understanding of what threatens MI and suggest a friendly revision to the ABC (...) that addresses the objection (§3). I then consider a second objection: that the ABC cannot make sense of the MI of the _non-autonomous_. This objection appears fatal even to the revised ABC (§4). On that basis, I develop an alternative conception on which MI is grounded in a plurality of simpler capacities, namely, those for _affect_, _cognition_, and _volition_. Each of these more basic capacities grounds a set of fundamental interests, and they are for that reason worthy of protection even when they do not rise to the level of complexity necessary for autonomy (§5). This yields a fully general theory of MI that accounts for its manifestations in both the autonomous and the non-autonomous. (shrink)

The case for massively modular models of mind -- The architecture of animal minds -- Modules of the human mind -- Modularity and flexibility : the first steps -- Creative cognition in a modular mind -- The cognitive basis of science -- Distinctively human practical reason.

In 1936, G. Birkhoff and J. v. Neumann published an article with the title The logic of quantum mechanics'. In this paper, the authors demonstrated that in quantum mechanics the most simple observables which correspond to yes-no propositions about a quantum physical system constitute an algebraic structure, the most important proper ties of which are given by an orthocomplemented and quasimodular lattice Lq. Furthermore, this lattice of quantum mechanical proposi tions has, from a formal point of view, many similarities with (...) a Boolean lattice L8 which is known to be the lattice of classical propositional logic. Therefore, one could conjecture that due to the algebraic structure of quantum mechanical observables a logical calculus Q of quantum mechanical propositions is established, which is slightly different from the calculus L of classical propositional logic but which is applicable to all quantum mechanical propositions. This calculus has sometimes been called 'quan tum logic'. However, the statement that propositions about quantum physical systems are governed by the laws of quantum logic, which differ from ordinary classical logic and which are based on the empirically well-established quantum theory, is exposed to two serious objec tions: Logic is a theory which deals with those relationships between various propositions that are valid independent of the content of the respective propositions. Thus, the validity of logical relationships is not restricted to a special type of proposition, e. g. to propositions about classical physical systems. (shrink)

ABSTRACT Tensism is the view that tense is not merely a property of language and the mind, but of the world itself. Perspectivalism extends this idea to all perspectival properties be they person or locational. One challenge that perspectivalism faces is the problem of expressing the contents of the beliefs and utterances of persons that are in other perspectival positions. One proposed solution to this problem is to allow for semantic theories that "realign" the expression of contents so that the (...) contents expressed by persons in other perspectival positions can be re-expressed from one's own perspectival position. In this paper I argue that a similar semantic realignment strategy could be deployed in helping perspectivalists generally come to grips with a puzzle raised by the Special Theory of Relativity. In short, the strategy is to realign the expression of contents in another inertial frame so that they are expressed from within your inertial frame. As we will see, the strategy is not puzzle free. (shrink)

This chapter examines the extent to which there are continuities between the cognitive processes and epistemic practices engaged in by human hunter-gatherers, on the one hand, and those which are distinctive of science, on the other. It deploys anthropological evidence against any form of 'no-continuity' view, drawing especially on the cognitive skills involved in the art of tracking. It also argues against the 'child-as-scientist' accounts put forward by some developmental psychologists, which imply that scientific thinking is present in early infancy (...) and universal amongst humans who have sufficient time and resources to devote to it. In contrast, a modularist kind of 'continuity' account is proposed, according to which the innately channelled architecture of human cognition provides all the materials necessary for basic forms of scientific reasoning in older children and adults, needing only the appropriate sorts of external support, social context, and background beliefs and skills in order for science to begin its advance. (shrink)

MONTAIGNE criou um novo gênero literário – o ensaio -, seus próprios Ensaios tiveram uma vasta influência sobre o pensamento e a literatura do Renascimento e dos séculos posteriores. Observador sereno e irônico da comédia humana, era notavelmente muito consciente do etnocentrismo de outros povos. Atraído pela diversidade humana, estava preparado para tomar a vida privada tão seriamente quanto a vida pública. MONTAIGNE tem sido muito freqüentemente tratado como um “moderno” nascido fora de sua época. Peter Burke apresenta-o como (...) um cavalheiro do campo, um homem do Renascimento e um membro da geração dos anos 1530 que floresceu numa sociedade dividida pela guerra civil, descreve as reações da posteridade aos Ensaios e pergunta se MONTAIGNE pode, em algum sentido, ser considerado nosso contemporâneo. (shrink)

This paper details the ontological and epistemic character of activties that occur in mechanisms. It explains why they are sufficient to handle the problems of causation.

New developments in reproductive technology have made headlines since the birth of the world's first in vitro fertilization baby in 1978. But is embryo experimentation ethically acceptable? What is the moral status of the early human embryo? And how should a democratic society deal with so controversial an issue, where conflicting views are based on differing religious and philosophical positions? These controversial questions are the subject of this book, which, as a current compendium of ideas and arguments on the subject, (...) makes an original contribution of major importance to this debate. (shrink)

End-of-life issues and questions are complex and frequently cause confusion and anxiety. In _Death with Dignity_,_ _theologian, medical ethicist, and pastoral caregiver Peter A. Clark examines numerous issues that are pertinent to patients, family members, and health care professionals, including physiology, consciousness, the definition of death, the distinction between extraordinary and ordinary means, medical futility, “Do Not Resuscitate” orders, living wills, power of attorney, pain assessment and pain management, palliative and hospice care, the role of spirituality in end-of-life care, (...) and physicians’ communication with terminal patients. Patients, family members, medical students, and health care professionals will find in _Death with Dignity _the_ _practical and ethical knowledge they need to capably and confidently cope with end-of-life challenges. (shrink)

Early modern experimental philosophers were opposed to speculation, and yet many endorsed speculative theories. This chapter gives a partial explanation of why this is so, using Robert Boyle’s acceptance and promotion of the corpuscular philosophy as a case study. It argues that, in addition to furnishing experimental evidence for the corpuscular hypothesis in his Forms and Qualities, Boyle attempted to establish its epistemic superiority over other speculative theories on the grounds that it is founded upon superior principles. In his ‘Excellency (...) and Grounds of the Mechanical Hypothesis’, Boyle claims that the principles of the corpuscular philosophy are more intelligible, more parsimonious, ontologically primary, simpler and more comprehensive than those of its rivals. On grounds of comparative plausibility then, according to Boyle, the corpuscular philosophy is eminently preferable to its rivals. The final section of the chapter traces the legacy of Boyle’s appraisal of the epistemic status of the corpuscular philosophy in the writings of many of his compatriots from the mid-1660s to the Cyclopedia of Ephraim Chambers of 1728. (shrink)

In A Professor's Duties, distinguished philosopher Peter J. Markie adds to the expanding discussion of the ethics of college teaching. Part One concentrates on the obligations of individual professors, primarily with regard to issues about what and how to teach. Part Two expands Professor Markie's views by providing a selection of the most significant previously published writings on the ethics of college teaching.

This chapter is offered as a contribution to the logic of down below. We attempt to demonstrate that the nature of human agency necessitates that there actually be such a logic. The ensuing sections develop the suggestion that cognition down below has a structure strikingly similar to the physical structure of quantum states. In its general form, this is not an idea that originates with the present authors. It is known that there exist mathematical models from the cognitive science of (...) cognition down below that have certain formal similarities to quantum mechanics. We want to take this idea seriously. We will propose that the subspaces of von Neumann-Birkhoff lattices are too crisp for modelling requisite cognitive aspects in relation to subsymbolic logic. Instead, we adopt an approach which relies on projections into nonorthogonal density states. The projection operator is motivated from cues which probe human memory. (shrink)

This volume critically explore and extend Hayek's Nobel Prize-winning work on knowledge and social interconnectedness from the disciplines of law, economics, philosophy, anthropology, political science, and history. Hayek's insights about knowledge become even more important once it is recognized that nothing in the social world occurs in isolation. There is no such thing as a distinct economic, political, or social sphere--they are inextricably intertwined. Given the range of both Hayek's work and the contributing authors' perspectives, the range of topics covered (...) in this volume is extraordinarily wide, running the gamut from immigration, to white supremacy, to ancient agricultural practices, to the nature of what it means to be free. (shrink)

An introduction to the life and work of the philosopher Jacques Derrida.

In this major study, Peter Zarrow examines how textbooks published for the Chinese school system played a major role in shaping new social, cultural, and political trends, the ways in which schools conveyed traditional and 'new style' knowledge and how they sought to socialize students in a rapidly changing society in the first decades of the twentieth century. Focusing on language, morality and civics, history, and geography, Zarrow shows that textbooks were quick to reflect the changing views of Chinese (...) elites during this period. Officials and educators wanted children to understand the physical and human worlds, including the evolution of society, the institutions of the economy, and the foundations of the nation-state. Through textbooks, Chinese elites sought ways to link these abstractions to the concrete lives of children, conveying a variety of interpretations of enlightenment, citizenship, and nationalism that would shape a generation as modern citizens of a new China. (shrink)

The paper discusses the question whether T-theories explain how it is possible to understand new sentences, or learn an infinite language, as Davidson claimed. I argue against some commentators that for explanatory power we need not require that T-theories are implicitly known or mirror cognitive structures. I note contra Davidson that the recursive nature of T-theories is not sufficient for explanatory power, since humans can work out only what is computationally tractable, and recursiveness by itself allows for intractable computational complexity. (...) I finally consider the complexity of T-theories, transformed into term rewriting systems, and find that the complexity of such systems is indeed tractable. Therefore Davidson's claim stands, even though a further condition had to be met. (shrink)