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; 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 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)

This essay is a critical discussion of the meta-ethical book "Ethics. Inventing Right and Wrong" by J.L.Mackie published in Harmondsworth, 1977. It is based on the German translation "Ethik. Auf der Suche nach dem Richtigen und Falschen, Stuttgart: Reclam 1983. The essay had been published in the German philosophical journal LOGOS (N.F. 3, 1996) and is written in German. There had been no abstract.

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

It may be safely asserted that few of the fragments of Greek lyric poetry have excited more discussion than the so-called ‘Lament of Danae’ but it is curious, considering that we owe our knowledge of it to Dionysius's desire to set his readers a metrical puzzle, to see how little attention has been given to the metre of the fragment by the many scholars who have contributed to the literature of the problem since 1835. The purpose of the present study (...) is to enquire into the scansion of the fragment, quoting parallels wherever possible from the extant remains of Simonides and, where these fail, from the works of other lyric poets. (shrink)

What happens when someone acts? A familiar answer goes like this. There is something that the agent wants, and there is an action that he believes conducive to its attainment. His desire for the end, and his belief in the action as a means, justify taking the action, and they jointly cause an intention to take it, which in turn causes the corresponding movements of the agent's body. I think that the standard story is flawed in several respects. The flaw (...) that will concern me in this paper is that the story fails to include an agent-or, more precisely, fails to cast the agent in his proper role. (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 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)

Managers tasked with organizational change often face irreconcilable demands on how to enact justice—situations we call _justice conundrums_. Drawing on interviews held with managers before and after a planned large-scale change, we identify specific conundrums and illustrate how managers grapple with these through three prototypical paths. Among our participants, the paths increasingly diverged over time, culminating in distinct career decisions. Based on our findings, we develop an integrative process model that illustrates how managers grapple with justice conundrums. Our contributions are (...) threefold. First, we elucidate three types of justice conundrums that managers may encounter when enacting justice in the context of planned organizational change (the justice intention-action gap, competing justice expectations, and the justice of care vs. managerial-strategic justice) and show how managers handle them differently. Second, drawing on the motivated cognition and moral disengagement literature, we illustrate how cognitive mechanisms coalesce to allow managers to soothe their moral (self-) concerns when grappling with these conundrums. Third, we show how motivated justice intentions ensuing from specific justice motives, moral emotions, and circles of moral regard predict the types of justice conundrums managers face and the paths they take to grapple with them. (shrink)

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)

Providing an original and systematic treatment of foundational issues in philosophy of religion, J. L. Schellenberg's new book addresses the structure of..

In recent years, millions of citizens all over the world have used digital dating services. It remains unknown to what extent human sexuality will be changed by this. Based on an evolutionary psychological perspective, we assume that sexual selection shaped behavioural tendencies in men and women that are designed to increase the reproductive fitness. These tendencies are referred to as sexual strategies. Males and females sexual strategies differ according to sex-dimorphic reproductive investments. We assume that this inheritance will affect human (...) sexuality also in a digital future. To evaluate this assumption, we conducted a selective review of studies on digital dating services. Based on sexual selection theory, we derived a number of hypotheses regarding how men and women will use digital dating services typically and how the use of digital dating services might affect sexual wellbeing. Out of an initial data set of 2,568 records, we finally reviewed a set of 13 studies. These studies provided support for the notion that men and women act in the digital dating area according to sex-typical strategies. However, sometimes the circumstances of digital dating affect communication flow, e.g., in that men are even more active in establishing contacts than they are in real world conditions. Overall, women appear to accomplish their sexual goals in digital dating arenas more than men do given a surplus of male demand. Our results suggest that future human sexuality will be impacted by an interaction of both: sex-dimorphic ancient sexual strategies and new technologies. (shrink)

Abstract I argue that meaning in life is importantly influenced by bioloical ties. More specifically, I maintain that knowing one's relatives and especially one's parents provides a kind of self-knowledge that is of irreplaceable value in the life-task of identity formation. These claims lead me to the conclusion that it is immoral to create children with the intention that they be alienated from their bioloical relatives?for example, by donor conception.

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)

Although the literature on organizational justice enactment is becoming richer, our understanding of the role of the deontic justice motive remains limited. In this article, we review and discuss theoretical approaches to and evidence of the deontic justice motive and deontic justice enactment. While the prevalent understanding of deontic justice enactment focuses on compliance, we argue that this conceptualization is insufficient to explain behaviors that go beyond the call of duty. We thus consider two further forms of deontic behavior: humanistic (...) and supererogatory behavior. Drawing on the concepts of situation strength and person strength, we further argue that the reduced variance in behavior across morally challenging situations makes deontic justice enactment visible. We thus observe deontic justice enactment when an actor’s deontic justice motive collides with strong situational cues or constraints that guide the actor to behave differently. We formulate propositions and develop a theoretical model that links the deontic justice motive to moral maturation and deontic justice enactment. (shrink)

Retributive theories of punishment argue that punishing a criminal for a crime she committed is sufficient reason for a justified and morally permissible punishment. But what about when the state gets lucky in its decision to punish? I argue that retributive theories of punishment are subject to “Gettier” style cases from epistemology. Such cases demonstrate that the state needs more than to just get lucky, and as these retributive theories of punishment stand, there is no anti-luck condition. I’ll argue that (...) Gettier-style cases demonstrate an impermissible instance of punishment, even though they meet the conditions of retributive theories of punishment. Retributive theories are, therefore, too weak. The safety condition from epistemology provides the anti-luck condition needed for permissible punishment. I argue that two forms of retributivism, rights-forfeiture and what I call standard retributivism, are both subject to Gettier-style cases. Unlike the literature on standards of proof, this paper argues that safety is a condition on punishment itself, i.e., in all nearby possible worlds, the accuser must correctly accuse the convicted for the crime they actually committed. (shrink)

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

Supervaluationism is often described as the most popular semantic treatment of indeterminacy. There’s little consensus, however, about how to fill out the bare-bones idea to include a characterization of logical consequence. The paper explores one methodology for choosing between the logics: pick a logic thatnorms beliefas classical consequence is standardly thought to do. The main focus of the paper considers a variant of standard supervaluational, on which we can characterizedegrees of determinacy. It applies the methodology above to focus ondegree logic. (...) This is developed first in a basic, single-premise case; and then extended to the multipremise case, and to allowdegreesof consequence. The metatheoretic properties of degree logic are set out. On the positive side, the logic is supraclassical—all classical valid sequents are degree logic valid. Strikingly, metarules such as cut and conjunction introduction fail. (shrink)

Hailed by the Bulletin of the American Mathematical Society as "undoubtedly a major addition to the literature of mathematical logic," this volume examines the essential topics and theorems of mathematical reasoning. No background in logic is assumed, and the examples are chosen from a variety of mathematical fields. Starting with an introduction to symbolic logic, the first eight chapters develop logic through the restricted predicate calculus. Topics include the statement calculus, the use of names, an axiomatic treatment of the statement (...) calculus, descriptions, and equality. Succeeding chapters explore abstract set theory—with examinations of class membership as well as relations and functions—cardinal and ordinal arithmetic, and the axiom of choice. An invaluable reference book for all mathematicians, this text is suitable for advanced undergraduates and graduate students. Numerous exercises make it particularly appropriate for classroom use. (shrink)

J.L. Schellenberg offers a path to a new kind of religious outlook. Reflection on our early stage in the evolutionary process leads to skepticism about religion, but also offers a new answer to the problem of faith and reason, and the possibility of a new, evolutionary form of religion.

Ultimism and the aims of human immaturity -- Faith without details, or how to practice skeptical religion -- Simple faith and the complexities of tradition -- The structure of faith justification -- How skeptical faith is true to reason -- Anselm's idea -- Leibniz's ambition -- Paley's wonder -- Pascal's wager -- Kant's postulate -- James's will -- Faith is positively justified : the many modes of religious vision.

This paper offers an alternate explanation of cases from the doxastic wronging literature. These cases violate what I call the degree of inquiry right—a novel account of zetetic obligations to inquire when interests are at stake. The degree of inquiry right is a moral right against other epistemic agents to inquire to a certain threshold when a belief undermines one’s interests. Thus, the agents are sometimes obligated to leave inquiry open. I argue that we have relevant interests in reputation, relationships, (...) and the well-being of our social groups. These interests generate obligations against others to “do their homework” before closing inquiry. This alternate account makes better sense of puzzles that accounts of doxastic wronging fall prey to. (shrink)

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)

According to anti-individualism, the basic building blocks of the world are not individuals. The anti-individualist argues that standard, individual-entailing claims–for instance, that Theia is a cat–are mistaken in presupposing that there are individuals, but that such claims correspond to statements in a feature-placing language devoid of these presuppositions. Instead, the world is entirely made up of non-individualistic features–structurally akin to familiar examples such as it's raining or it's snowing–that are arranged in particular ways. Since features do not carve out individual (...) differences, however, this seems to entail that there is a class of statements in an individualistic language–statements expressing mere differences in which object is which–the members of which all correspond to the same anti-individualist description. That is, anti-individualism seems to entail anti-haecceitism, according to which all differences in ways the world could be supervene on qualitative differences. In this paper, I argue that, on the contrary, the anti-individualist has the resources to accommodate non-qualitative differences among ways the world could be. Moreover, haecceitistic anti-individualism does justice to the motivations for rejecting individuals while nevertheless accommodating intuitions that certain kinds of scenarios are metaphysically distinct. (shrink)