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)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (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)

It is common to hear talk of the aim of belief and to find philosophers appealing to that aim for numerous explanatory purposes. What belief 's aim explains depends, of course, on what that aim is. Many hold that it is somehow related to truth, but there are various ways in which one might specify belief 's aim using the notion of truth. In this article, by considering whether they can account for belief 's standard of correctness and the epistemic (...) norms governing belief, I argue against certain prominent specifications of belief 's aim given in terms of truth, and advance a neglected alternative. (shrink)

Simon May has argued that the notion of a principled compromise is incoherent. Reasons to compromise are always in his view strategic: though we think that the position we defend is still the right one, we compromise on this view in order to avoid the undesirable consequences that might flow from not compromising. I argue against May that there are indeed often principled reasons to compromise, and that these reasons are in fact multiple. First, compromises evince respect for persons that (...) we have reason to think of as our epistemic peers, and acknowledgement of our own finitudes as moral reasoners. Second, compromises are often made morally necessary by the shortfalls that unavoidably separate democratic institutions from democratic ideals. Third, compromises express a desirable form of democratic community. And fourth, compromises are often justified from a consequentialist point of view, in that they allow for the realization of values that would not be realized as well by the failure to compromise. (shrink)

Plato's dialogues frequently criticize traditional Greek myth, yet Plato also integrates myth with his writing. Daniel S. Werner confronts this paradox through an in-depth analysis of the Phaedrus, Plato's most mythical dialogue. Werner argues that the myths of the Phaedrus serve several complex functions: they bring nonphilosophers into the philosophical life; they offer a starting point for philosophical inquiry; they unify the dialogue as a literary and dramatic whole; they draw attention to the limits of language and the limits (...) of knowledge; and they allow Plato to co-opt cultural authority as a way of defining and legitimating the practice of philosophy. Platonic myth, as a species of traditional tale, is thus both distinct from philosophical dialectic and similar to it. Ultimately, the most powerful effect of Platonic myth is the way in which it leads readers to participate in Plato's dialogues and to engage in a process of self-examination. (shrink)

This paper defends the epistemic account of the normativity of requests. The epistemic account says that a request does not create any reasons and thus does not have any special normative power. Rather, a request gives reasons by revealing information which is normatively relevant. I argue that compared to competing accounts of request normativity, especially those of David Enoch and James H.P. Lewis, the epistemic account gives better answers to cases of insincere requests, is simpler, and does a better job (...) incorporating the importance of relationships. I also defend the epistemic account from three objections: that requests are important because they constitute consent, that requests and wishes must be normatively different, and that some requests do not provide any new information. (shrink)

The U.S. election in November 2016 raised and amplified doubts about first-past-the-post (“plurality rule”) electoral systems. Arguments against plurality rule and for alternatives like preferential voting tend to be consequentialist: it is argued that systems like preferential voting produce different, better outcomes. After briefly noting why the consequentialist case against plurality rule is more complex and contentious than it first appears, I offer an expressive alternative: plurality rule produces actual or apparent dilemmas for voters in ways that are morally objectionable, (...) and avoidable under preferential voting systems. This expressive case against plurality rule is both simpler and more ecumenical than its consequentialist counterpart, and it provides strong reasons to prefer alternatives to plurality rule. Moreover, it suggests a distinct way of evaluating different alternatives like preferential voting. (shrink)

Supporters of open borders sometimes argue that the state has no pro tanto right to restrict immigration, because such a right would also entail a right to exclude existing citizens for whatever reasons justify excluding immigrants. These arguments can be defeated by suggesting that people have a right to stay put. I present a new form of the exclusion argument against closed borders which escapes this “right to stay put” reply. I do this by describing a kind of exclusion that (...) has not been discussed in depth, which I call “territorial exclusion.” Territorial exclusion is the process according to which the group that wishes to exclude current citizens secedes from the territory in which those citizens reside. I argue that the wrongness of territorial exclusion explains why there is no pro tanto right for a state to exclude immigrants, because otherwise there would be a pro tanto right for the state to kick people out by seceding from the territory they inhabit. Because kicking people out like this is typically wrong, borders cannot be closed. (shrink)

I ask you to X. You now have a reason to X. My request gave you a reason. How? One unpopular theory is the epistemic account, according to which requests do not create any new reasons but instead simply reveal information. For instance, my request that you X reveals that I desire that you X, and my desire gives you a reason to X. Peter Schaber has recently attacked both the epistemic account and other theories of the reason-giving force of (...) requests. Schaber defends a new theory of the reason-giving force of requests according to which request give reasons because it is valuable for requesters and requestees that requests have this power. In this paper I argue that Schaber's attack on the epistemic account fails, and that his own theory ought to be rejected because it faces compelling objections. (shrink)

“X-Firsters” hold that there is some normative feature that is fundamental to all others (and, often, that there’s some normative feature that is the “mark of the normative”: all other normative properties have it, and are normative in virtue of having it). This view is taken as a starting point in the debate about which X is “on first.” Little has been said about whether or why we should be X-Firsters, or what we should think about normativity if we aren’t (...) X-Firsters. Hence the chapter’s two main goals. First, to provide a simple argument that one shouldn’t be an X-Firster about the normative domain, which starts with the observation that analogous views have dubious merits in analogous domains. Second, to offer an alternative view—taking normativity to be a determinable explained in terms of its determinates—that offers an interesting way to think about the structure and unity of normativity. (shrink)

Motion—and, in particular, local motion or change in location—plays a central role in Kenelm Digby’s natural philosophy and in his arguments for the immateriality of the soul. Despite this, Digby’s account of what motion consists in has yet to receive much scholarly attention. In this paper, I advance a novel interpretation of Digby on motion. According to it, Digby holds that for a body to move is for it to divide from and unify with other bodies. This is a view (...) of motion—as change in relations of parthood—that Alison Peterman attributes to Digby’s contemporary and acquaintance, Margaret Cavendish. Having shown that Digby’s presentation of the view predates Cavendish’s by more than a decade, I make a case that Digby’s work influenced Cavendish’s on this topic. In developing and defending my reading, I consider to what extent the Digbean account of motion and the arguments for it accord with the ideals of the mechanical philosophy emerging in the early modern period. (shrink)

I defend the cosmopolitan instrumentalist theory of secession, according to which a group has a right to secede only if this would promote cosmopolitan justice. I argue that the theory is preferable to other theories of secession because it is an entailment of cosmopolitanism, which is independently attractive, and because, unlike other theories of secession, it allows us to give the answers we want to give in cases like secession of the rich or secession that would make things worse for (...) minorities. I defend the view against the objections that it allows for colonialism and annexation, that it is not a distinct theory, and that it is impractical. (shrink)

Die Generation der deutschen Spätaufklärung galt nach ihrer Selbstinterpretation als Vertreter einer neuen Zeit, in der das Bürgertum - die Klasse, mit der sie paktierten, - den künftigen Lauf der Geschichte zu bestimmen habe. Ihre Monatsschrift war das Medium einer Vermittlung zwischen Theorie und Praxis. Indem die Aufklärer das reaktionäre Potential des absolutistischen Staates unterschätzten und den Willen ihres bürgerlichen Publikums zum Selbstdenken überschätz- ten, büssten sie ihre Führungsrolle ein. Staat und Gesellschaft wehrlos ausgeliefert, hat die Generation der Spätaufklärung Aktualität (...) als Paradigma einer gescheiterten Intelligenzschicht. (shrink)

Abstract This paper offers an appraisal of Phillip Pettit's approach to the problem how a merely finite set of examples can serve to represent a determinate rule, given that indefinitely many rules can be extrapolated from any such set. I argue that Pettit's so-called ethnocentric theory of rule-following fails to deliver the solution to this problem he sets out to provide. More constructively, I consider what further provisions are needed in order to advance Pettit's general approach to the problem. I (...) conclude that what is needed is an account that, whilst it affirms the view that agents' responses are constitutively involved in the exemplification of rules, does not allow such responses the pride of place they have in Pettit's theory. (shrink)

This book is a study of the role of intellect in human action as described by Thomas Aquinas. One of its primary aims is to compare the interpretation of Aristotle by Aquinas with the lines of interpretation offered in contemporary Aristotelian scholarship. The book seeks to clarify the problems involved in the appropriation of Aristotle's theory by a Christian theologian, including such topics as the practical syllogism and the problems of akrasia. Westberg argues that Aquinas was much closer to Aristotle (...) than is often recognized, and he puts forward important new interpretations of the relation of intellect and will in the stages of intention, deliberation, decision, and execution. In the concluding section of the book, he shows how this new interpretation yields fruitful insights on a range of theological topics, including sin, law, love, and the moral virtues. (shrink)

Mandatory minimum sentencing provisions have been a feature of the U.S. justice system since 1790. But they have expanded considerably under the war on drugs, and their use has expanded considerably under the Trump Administration; some states are also poised to expand drug-related mandatory minimums further in efforts to fight the current opioid epidemic. In this paper I outline and evaluate three prominent arguments for and against the use of mandatory minimums in the war on drugs—they appeal, respectively, to proportionality, (...) consistency, and efficiency. I ultimately defend the view that the use of mandatory minimums in the war on drugs is unjust. -/- . (shrink)

This paper aims to understand Hegel’s claim in the introduction to his Philosophy of Mind that mind is an actualization of the Idea and argues that this claim provides us with a novel and defensible way of understanding Hegel’s naturalism. I suggest that Hegel’s approach to naturalism should be understood as ‘formal’, and argue that Hegel’s Logic, particularly the section on the ‘Idea’, provides us with a method for this approach. In the first part of the paper, I present an (...) interpretation of Hegel’s method in which life plays a central role. In the second part of the paper, I develop Hegel’s method by providing a reading of Hegel’s Subjective Spirit, focusing on the sections ‘Anthropology’ and ‘Phenomenology’ in particular, arguing that they display the dialectic between life and cognition outlined by Hegel’s Idea. (shrink)

This paper aims to understand Hegel’s claim in the introduction to his Philosophy of Mind that mind is an actualization of the Idea and argues that this claim provides us with a novel and defensible way of understanding Hegel’s naturalism. I suggest that Hegel’s approach to naturalism should be understood as ‘formal’, and argue that Hegel’s Logic, particularly the section on the ‘Idea’, provides us with a method for this approach. In the first part of the paper, I present an (...) interpretation of Hegel’s method in which life plays a central role. In the second part of the paper, I develop Hegel’s method by providing a reading of Hegel’s Subjective Spirit, focusing on the sections ‘Anthropology’ and ‘Phenomenology’ in particular, arguing that they display the dialectic between life and cognition outlined by Hegel’s Idea. (shrink)

Can a liberal state exclude illiberal immigrants in order to preserve its liberal status? Hrishikesh Joshi has argued that liberalism cannot require a commitment to open borders because this would entail that liberalism is committed to its own demise in circumstances in which many illiberal immigrants aim to immigrate into a liberal society. I argue that liberalism is committed to its own demise in certain circumstances, but that this is not as bad as it may appear. Liberalism’s commitment to its (...) own demise is merely a reflection of the fact that it must take into account the rights of outsiders, not just the rights of existing citizens, and of the fact that circumstances of injustice can sometimes leave liberal societies with no correct choice. (shrink)

This essay considers the critical response to Hegel's view of Socrates we find in Kierkegaard's dissertation, The Concept of Irony. I argue that this dispute turns on the question whether or not the examination of particular thinkers enters into Socrates’ most basic aims and interests. I go on to show how Kierkegaard's account, which relies on an affirmative answer to this question, enables him to provide a cogent defence of Socrates' philosophical practice against Hegel's criticisms.

Lovejoy (1873-1962) was America's foremost historian of ideas, a major participant in the philosophical debates of the twentieth century, and a prominent advocate of academic freedom. The product of an emotionally unsettled childhood and an evangelical father, Lovejoy reacted against his father by postulating the certainty of self-sufficient reason. He believed that only the principles of reason could order the world and so make our universe intelligible. Originally published in 1980. A UNC Press Enduring Edition -- UNC Press Enduring Editions (...) use the latest in digital technology to make available again books from our distinguished backlist that were previously out of print. These editions are published unaltered from the original, and are presented in affordable paperback formats, bringing readers both historical and cultural value. (shrink)

According to ethical objectivism, what a person should do depends on the facts, as opposed to their perspective on the facts. A long-standing challenge to this view is that it fails to accommodate the role that norms play in guiding a person’s action. Roughly, if the facts that determine what a person should do lie beyond their ken, they cannot inform a person’s deliberations. This paper explores two recent developments of this line of thought. Both focus on the epistemic counterpart (...) to ethical objectivism, according to which what a person should believe depends on the facts, as opposed to their perspective on the facts. The suggestion in each case is that epistemic objectivism faces a distinctive problem in accommodating guidance. Insofar as objectivism concerning the epistemic domain stands or falls with objectivism concerning the ethical domain, this is a problem for objectivism more generally. In this paper, I show that those arguments are not successful. The upshot is that the objectivist – whether ethical or epistemic – need not reject the idea that norms serve a guiding function. (shrink)

Schober et al. describe two studies on how survey interview respondents misunderstand interview questions. After answering a survey, participants are given standardized definitions of the questions they have just answered. Even apparently simple questions such as “Have you smoked more than 100 cigarettes?” are interpreted very differently by participants. Moreover, clarifying the meaning of the definitions with the interviewer does not always help resolve the miscommunication.