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)

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.

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)

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)

Berkeley’s likeness principle is the claim that “an idea can be like nothing but an idea”. The likeness principle is intended to undermine representationalism: the view (that Berkeley attributes to thinkers like Descartes and Locke) that all human knowledge is mediated by ideas in the mind which represent material objects. Yet, Berkeley appears to leave the likeness principle unargued for. This has led to several attempts to explain why Berkeley accepts it. In contrast to ‘metaphysical’ and ‘epistemological’ interpretations available in (...) the literature, in this paper I defend a ‘conceptual’ interpretation. I argue that Berkeley accepts the likeness principle on the basis of (i) his commitment to the transparency of ideas, and (ii) his account of resemblance which he sets out in his works on vision. Thus, I provide an explanation for Berkeley’s reasons for accepting the likeness principle which, appropriately, focuses on his views concerning ideas and likeness. (shrink)

When do two sentences say the same thing, that is, express the same content? We defend two-component (2C) semantics: the view that propositional contents comprise (at least) two irreducibly distinct constituents, (1) truth-conditions, and (2) subject-matter. We contrast 2C with one-component (1C) semantics, focusing on the view that subject-matter is reducible to truth- conditions. We identify exponents of this view and argue in favor of 2C. An appendix proposes a general formal template for propositional 2C semantics.

According to the authors of Populism and Civil Society, ‘populism is situated within the democratic imaginary’ but its logic is authoritarian. This article agrees with the first but challenges the second argument by focussing on the question of representation. In the case of ‘populism as government’ the tensions between bottom-up and top-down articulations seem to be more or less resolved by the repression of bottom-up organization, but in so doing, so the argument of this article, populism is mutating into something (...) else. Furthermore, ‘populist dictatorship’ seems to be closer to a dictatorship strategically using populist tools than to an intrinsic populist logic. While I agree with the authors on the authoritarian cases of populism in government, my argument diverges from the book when it comes to populism as government and introduces a discussion about the nature of populism. To this purpose, I first propose a complex definition of populism which understands populism not as the essence, but as one component of hybrid authoritarian formations, thus enabling the disentanglement of populism, authoritarianism, and totalitarianism. Second, I examine two components of populism that Arato and Cohen lay out in the book: the specific representation pars pro toto and embodiment. Building on Lefort, I argue that these components are not populist but totalitarian and that the empirical manifestations of populism are always hybrid, mixing populist and authoritarian or even totalitarian components. (shrink)

Margaret Macdonald was at the institutional heart of analytic philosophy in Britain in the mid-twentieth century. Yet, her views on the nature of philosophical theories diverge quite considerably from those of many of her contemporaries. In this paper, I focus on her 1953 article ‘Linguistic Philosophy and Perception’, a provocative paper in which Macdonald argues that the value of philosophical theories is more akin to that of poetry or art than science or mathematics. I do so for two reasons. First, (...) because it reveals just how far Macdonald’s meta- philosophical views diverged from those of many of her contemporaries. Second, because the discussion in LPP pre-empts recent literature on the nature of philosophical inquiry and the efficacy of philosophical arguments. Indeed, Macdonald’s paper is just as likely to provoke discussion today as it was in the 1950s. (shrink)

It is argued that causal understanding originates in experiences of acting on objects. Such experiences have consistent features that can be used as clues to causal identification and judgment. These are singular clues, meaning that they can be detected in single instances. A catalog of 14 singular clues is proposed. The clues function as heuristics for generating causal judgments under uncertainty and are a pervasive source of bias in causal judgment. More sophisticated clues such as mechanism clues and repeated interventions (...) are derived from the 14. Research on the use of empirical information and conditional probabilities to identify causes has used scenarios in which several of the clues are present, and the use of empirical association information for causal judgment depends on the presence of singular clues. It is the singular clues and their origin that are basic to causal understanding, not multiple instance clues such as empirical association, contingency, and conditional probabilities. (shrink)

In this important new book in the IPPP series, a group of leading thinkers in psychiatry, psychology, and philosophy offer alternative perspectives that address both the scientific and clinical aspects of psychiatric validation, emphasizing throughout their philosophical and historical considerations.

William Molyneux was born in Dublin, studied in Trinity College Dublin, and was a founding member of the Dublin Philosophical Society (DPS), Ireland’s counterpart to the Royal Society in London. He was a central figure in the Irish intellectual milieu during the Early Modern period and – along with George Berkeley and Edmund Burke – is one of the best-known thinkers to have come out of that context and out of Irish thought more generally. In 1688, when Molyneux wrote the (...) letter to Locke in which he posed the now famous question about a man born blind made to see, he was an active member of the DPS and was on familiar terms with several other key figures in Irish philosophy at the time. For the most part, Irish thinkers in the seventeenth and eighteenth centuries answered “no” to Molyneux’s question of whether a blind man made to see could distinguish, by sight alone, between a cube and a sphere. (shrink)

ABSTRACTThe political is changing its shape. Ideologies are no longer stable, but instead build hybrid combinations. Populism is getting popular. In addition, there are new forms of political exper...

This paper provides a philosophical evaluation of the concept of handedness prevalent but largely unspoken in the scientific literature. This literature defines handedness as the preference or ability to use one hand rather than the other across a range of common activities. Using the philosophical discipline of phenomenology, I articulate and critique this conceptualization of handedness. Phenomenology shows defining a concept of handedness by focusing on hand use leads to a right hand biased concept. I argue further that a phenomenological (...) model based in spatial orientation rather than hand use provides a more inclusive concept of handedness. (shrink)

In my contribution to this Concise Collection on Margaret Cavendish, I focus on teaching Cavendish’s work in the context of philosophy (and, more specifically, Early Modern Philosophy). I have three aims. First, to explain why teaching women from philosophy’s history is crucially important to the discipline. Second, to outline my own reflections on teaching Cavendish’s philosophy. Third, to defend a specific claim about the benefits of teaching Cavendish to philosophy students; namely, that introducing biographical detail alongside philosophical ideas enriches the (...) learning experience. (shrink)

Since its original publication in 1975, this groundbreaking work has awakened millions of people to the existence of "speciesism"—our systematic disregard of nonhuman animals—inspiring a worldwide movement to transform our attitudes to animals and eliminate the cruelty we inflict on them. In Animal Liberation, author Peter Singer exposes the chilling realities of today’s "factory farms" and product-testing procedures—destroying the spurious justifications behind them, and offering alternatives to what has become a profound environmental and social as well as moral issue. (...) An important and persuasive appeal to conscience, fairness, decency, and justice, it is essential reading for the supporter and the skeptic alike. (shrink)

First of all some problems of a scientifical dialogue between the different systems in the East and the West are being presented. In such a dialogue symmetry and reflexivity as principles of orientation have an important function. These principles are close to reality in the field of the philosophy of science and history of science in the DDR. By the controversy between the philosophy of science and the history of science in the DDR and by the way of discussing the (...) Kuhnian theory within the Marxist-Leninist-philosophy of science, together with an apologetical demarcation a real westernoriented willingness of dialogue in the DDR can be remarked. Even farreaching positions can be found so that an intensification of the dialogue is possible. (shrink)

Prospect Theory: For Risk and Ambiguity, provides a comprehensive and accessible textbook treatment of the way decisions are made both when we have the statistical probabilities associated with uncertain future events and when we lack them. The book presents models, primarily prospect theory, that are both tractable and psychologically realistic. A method of presentation is chosen that makes the empirical meaning of each theoretical model completely transparent. Prospect theory has many applications in a wide variety of disciplines. The material in (...) the book has been carefully organized to allow readers to select pathways through the book relevant to their own interests. With numerous exercises and worked examples, the book is ideally suited to the needs of students taking courses in decision theory in economics, mathematics, finance, psychology, management science, health, computer science, Bayesian statistics, and engineering. (shrink)

P.F. Strawson's essay traces some formal characteristics of logic and grammar to their roots in general features of thought and experience.

Although we can observe noticeable progress in gender diversity on corporate boards, these boards remain far from gender balanced. Our paper builds on social identity theory to examine the impact of corporate elites—men and women who sit on multiple corporate boards—on board diversity. We extend the main argument of social identity theory concerning favouritism based on homophily by suggesting that boards with men with multiple appointments are unwilling to include female board members to protect the monopoly value generated by their (...) elite status. The empirical analysis, based on DAX 30 firms in the period of 2010–2015, shows that the presence of multi-board men is negatively associated with women’s participation, while the presence of multi-board women and other women on management boards is positively related to gender diversity on boards. Furthermore, robustness tests support and confirm our conclusion that multi-board men have a significant association with board diversity, even with small size. Additionally, we find a significant effect arising from pressure related to the introduction of gender quotas in Germany, effective in 2016, indicating the effectiveness of gender quota policies for board gender diversity. (shrink)

In der genannten Epoche werden Grundentscheidungen gefällt, welche die Fundamentalfrage der Philosophie, die Seinsfrage, in die Krisis führen, in den Nihilismus unter ontologischem, metaphysischem, epistemologischem, axiologischem Aspekt. Den Extrempositionen der Systemdenker Hegel, Schopenhauer und Schelling erwachsen in den Hegelkritikern Feuerbach, Br. Bauer, Marx und Stirner Kontrapositionen, die das Wahrheitsproblem der Beliebigkeit unterstellen. Kierkegaard klagt unter existentiellem Aspekt das Problem der Wahrheit ein. Nietzsche überholt durch Abschaffung der Wahrheit alle Positionen,was seinen Standort in der europäischen Denkgeschichte ausmacht und als Ergebnis der (...) problemgeschichtlichen Analysen zu charakterisieren ist. Die Rückgewinnung des Vernunfthorizontes setzen erst die Problemdenker N. Hartmann und M. Heidegger ins Werk durch kritische Erneuerung der Seinsfrage. (shrink)

In September 2008, the European Organization for Nuclear Research (CERN) scientists successfully switched on the historic biggest physics device, the Large ...

This study examines how institutional logics interplay in a cross-sector social partnership that manages refugee integration in a rural district in Germany. In an inductive 15-month case study that drew on interviews and observations, we observe the dynamic materialization of institutional logics in day-to-day practices and an increasing contradiction and even rivalry between community- and market-based institutional logics over time. As a result, we delineate a model explaining the interplay of institutional logics along two dimensions: the dominance of one salient (...) logic and whether conflicts arise among logics. Our analysis also addresses the unifying properties of community as an institutional logic, especially in the context of urgency conditions. In addition, we show the influence of exogenous events and their media coverage on the interplay and conflicts of institutional logics. By unfolding the complexity of refugee integration—one of the global grand challenges of the present—we deepen the current understanding of the specific challenges addressed by cross-sector social partnerships. (shrink)

"This book is an augmented and updated translation by the author of Theorie des Subjekts: Subjectiviteat und Identiteat zwischen Moderne und Postmoderne, Teubingen, Francke-UTB, 2010 (3rd ed.)"--Title page verso.

European Journal of Philosophy, Volume 30, Issue 2, Page 676-692, June 2022.

According to ontological nihilism there are, fundamentally, no individuals. Both natural languages and standard predicate logic, however, appear to be committed to a picture of the world as containing individual objects. This leads to what I call the \emph{expressibility challenge} for ontological nihilism: what language can the ontological nihilist use to express her account of how matters fundamentally stand? One promising suggestion is for the nihilist to use a form of \emph{predicate functorese}, a language developed by Quine. This proposal faces (...) a difficult objection, according to which any theory in predicate functorese will be a notational variant of the corresponding theory stated in standard predicate logic. Jason Turner (2011) has provided the most detailed and convincing version of this objection. In the present paper, I argue that Turner's case for the notational variance thesis relies on a faulty metasemantic principle and, consequently, that an objection long thought devastating is in fact misguided. (shrink)

An examination of topics involved in statistical reasoning with imprecise probabilities. The book discusses assessment and elicitation, extensions, envelopes and decisions, the importance of imprecision, conditional previsions and coherent statistical models.