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)

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)

“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)

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)

The potential to collect brain data more directly, with higher resolution, and in greater amounts has heightened worries about mental and brain privacy. In order to manage the risks to individuals posed by these privacy challenges, some have suggested codifying new privacy rights, including a right to “mental privacy.” In this paper, we consider these arguments and conclude that while neurotechnologies do raise significant privacy concerns, such concerns are—at least for now—no different from those raised by other well-understood data collection (...) technologies, such as gene sequencing tools and online surveillance. To better understand the privacy stakes of brain data, we suggest the use of a conceptual framework from information ethics, Helen Nissenbaum’s “contextual integrity” theory. To illustrate the importance of context, we examine neurotechnologies and the information flows they produce in three familiar contexts—healthcare and medical research, criminal justice, and consumer marketing. We argue that by emphasizing what is distinct about brain privacy issues, rather than what they share with other data privacy concerns, risks weakening broader efforts to enact more robust privacy law and policy. (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 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)

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)

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 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)

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)

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 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)

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.

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)

Chapter I: The Geometry of Visibles 1 . The N on- Euclidean Geometry of Visibles In the chapter "The Geometry of Visibles" in Inquiry into the Human Mind, ...

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)

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.

The _Physics_ is a foundational work of western philosophy, and the crucial one for understanding Aristotle's views on matter, form, essence, causation, movement, space, and time. This richly annotated, scrupulously accurate, and consistent translation makes it available to a contemporary English reader as no other does—in part because it fits together seamlessly with other closely associated works in the New Hackett Aristotle series, such as the _Metaphysics_, _De Anima_, and forthcoming _De Caelo_ and _On Coming to Be and Passing Away_. (...) Eventually the series will include all of Aristotle's works. Sequentially numbered endnotes provide the information most needed at each juncture, while a detailed Index of Terms indicates places where focused discussion of key notions occurs. An illuminating general Introduction describes the book that lies ahead, explaining what sort of work it is and what sorts of evidence it relies on. (shrink)

The almost 300 articles contain not only historical accounts but also some indication of the state of present day study in classical philosophy.

Despite myriad controversies about reasons, two theses are frequently taken for granted: (i) reasons are sources of normative support for actions, attitudes, etc; and (ii) reasons, at least in simple, paradigmatic cases, consist in atomic facts. Call this conjunction “the atomic view.” Against this, we advocate what we call “the cluster view,” on which even in the simplest cases, the normative support for an action or attitude is typically provided by a whole cluster of facts. Moreover, many of these facts (...) are on an explanatory par—they each play the same kind of role in explaining why there is normative support for the action or attitude in question. We show that presupposition of the atomic view generates unnecessary (psuedo-)puzzles⁠—about topics such as rationality, moral worth, and doxastic justification⁠—that can be largely (dis)solved with the cluster view in place. The cluster view’s ability to do this constitutes an argument in its favor, beyond intuitive considerations that we also adduce. (shrink)