The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

This book defends a form of ethical intuitionism, according to which (i) there are objective moral truths; (ii) we know some of these truths through a kind of immediate, intellectual awareness, or "intuition"; and (iii) our knowledge of moral truths gives us reasons for action independent of our desires. The author rebuts all the major objections to this theory and shows that the alternative theories about the nature of ethics all face grave difficulties.

The first edition of The Scientific Background to Modern Philosophy took the dialogue of science and philosophy from Aristotle through to Newton. This second edition adds eight chapters, taking the dialogue through the Enlightenment and up to Darwin. This anthology is an attempt to help bridge the gap between the history of science and the history of philosophy.

Part I: The representation of life -- Can life be given a real definition? -- The representation of the living individual -- The representation of the life-form itself -- Part II: Naive action theory -- Types of practical explanation -- Naive explanation of action -- Action and time -- Part III: Practical generality -- Two tendencies in practical philosophy -- Practices and dispositions as sources of the goodness of individual actions -- Practice and disposition as sources of individual action.

Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integrity of ontologies and reason over data annotated (...) with ontology terms to make inferences that promote knowledge discovery. Therefore, it is important not only to include in ontologies multiple types of definitions in both formal and in natural languages, but also to ensure that these definitions meet good quality standards so they are useful. While tools such as Protégé can assist in creating well-formed logical definitions, producing good definitions in a natural language is still to a large extent a matter of human ingenuity supported at best by just a small number of general principles. For lack of more precise guidelines, definition authors are often left to their own personal devices. This paper aims to fill this gap by providing the ontology community with a set of principles and conventions to assist in definition writing, editing, and validation, by drawing on existing definition writing principles and guidelines in lexicography, terminology, and logic. (shrink)

At the University of Sheffield during 2011 and 2012, a leading group of philosophers, psychologists, and others gathered to explore the nature and significance of implicit bias. The two volumes of Implicit Bias and Philosophy emerge from these workshops. Each volume philosophically examines core areas of psychological research on implicit bias as well as the ramifications of implicit bias for core areas of philosophy. Volume I: Metaphysics and Epistemology is comprised of two parts: “The Nature of Implicit Attitudes, Implicit Bias, (...) and Stereotype Threat,” and “Skepticism, Social Knowledge, and Rationality.” The first part contains chapters examining the relationship between implicit attitudes and “dual process” models of the mind; the role of affect in the formation and change of implicit associations; the unity (or disunity) of implicit attitudes; whether implicit biases are mental states at all; and whether performances on stereotype-relevant tasks are automatic and unconscious or intentional and strategic. The second part contains chapters examining implicit bias and skepticism; the effects of implicit bias on scientific research; the accessibility of social stereotypes in epistemic environments; the effects of implicit bias on the self-perception of members of stigmatized social groups as rational agents; the role of gender stereotypes in philosophy; and the role of heuristics in biased reasoning. (shrink)

Externalist theories of justification create the possibility of cases in which everything appears to one relevantly similar with respect to two propositions, yet one proposition is justified while the other is not. Internalists find this difficult to accept, because it seems irrational in such a case to affirm one proposition and not the other. The underlying internalist intuition supports a specific internalist theory, Phenomenal Conservatism, on which epistemic justification is conferred by appearances.

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.

In this engaging and spirited text, Michael Lynch argues that truth does matter, in both our personal and political lives. He explains that the growing cynicism over truth stems in large part from our confusion over what truth is.

Causation: A Realist Approach Traditional empiricist accounts of causation and laws of nature have been reductionist in the sense of entailing that given a complete specification of the non-causal properties of and relations among particulars, it is therefore logically determined both what laws there are and what events are causally related. It is argued here, however, that reductionist accounts of causation and of laws of nature are exposed to decisive objections, and thus that the time has come for empiricists to (...) break with that tradition. -/- The basic goal of this book, therefore, is to set out and defend realistic accounts of those concepts. In the case of causal relations, for example, Tooley maintains that causation is basically a matter of theoretical relations between states of affairs that underlie and explain relative frequencies. He also argues that such an approach avoids the objections that tell against reductionist accounts and that it does so without making causal relations epistemologically inaccessible. (shrink)

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.

Dignity plays a central role in current thinking about law and human rights, but there is sharp disagreement about its meaning. Combining conceptual precision with a broad historical background, Michael Rosen puts these controversies in context and offers a novel, constructive proposal. “Penetrating and sprightly...Rosen rightly emphasizes the centrality of Catholicism in the modern history of human dignity. His command of the history is impressive...Rosen is a wonderful guide to the recent German constitutional thinking about human dignity...[Rosen] is in (...) general an urbane and witty companion, achieving his aim of accessibly written philosophy.” —Samuel Moyn, The Nation “[An] elegant, interesting and lucid exploration of the concept of dignity...Drawing on classical, liberal and Catholic traditions, Rosen hopes to rehabilitate dignity to its rightful place near the centre of moral thought...Rosen's admirable book deserves wide attention from political theorists, jurisprudes and political philosophers.” —Simon Blackburn, Times Higher Education “Dignity deserves to be widely read, not only for its intrinsic interest, but also as a corrective to the habit of discussing such topics in abstraction from their social context. Whether or not one agrees with Rosen's arguments, there can be no doubt he has widened our horizons.” —Rae Langton, Times Literary Supplement. (shrink)

This volume of essays is an important introduction to the thought of one of the twentieth century's most significant yet underappreciated philosophers, Richard McKeon. The originator of philosophical pluralism, McKeon made extraordinary contributions to philosophy, to international relations, and to theory-formation in the communication arts, aesthetics, the organization of knowledge, and the practical sciences. This collection, which includes a philosophical autobiography as well as the out-of-print title essay "Freedom and History" and a previously unpublished essay on "Philosophic Semantics and Philosophic (...) Inquiry," is a testimony to the range and systematic power of McKeon's thinking for the social sciences and the humanities. (shrink)

edition (unseen), $12.95. traditions, bringing into being new modes of understanding. Paper Anthropology, and particularly ethnography, is torn between two quests, one to capture the diversity of social life and the other to discover universal principles structuring that diversity. Jackson examines these quests within the context of ethnographic fieldwork, focusing on the relationship between ethnographers and the people they study. He is concerned with defining the anthropological project as something more than the projection of the anthropologist's traditions and concerns onto (...) an alien culture. Rather, he would have the project open a genuine dialogue between people from different cultures or Annotation copyrighted by Book News, Inc., Portland, OR. (shrink)

Michael G. Titelbaum presents a new Bayesian framework for modeling rational degrees of belief—the first of its kind to represent rational requirements on agents who undergo certainty loss.

In this paper, I propose a new way of defining sport that I call a ‘core-periphery’ model. According to a core-periphery model, sport comes in degrees – what I refer to as ‘sport-likeness’ – and the aim of the philosopher of sport is to chart those dimensions along which an activity can be more or less a sport. By introducing the concept of sport-likeness, the core-periphery model complicates the picture of what is or is not a sport and encourages philosophers (...) interested in defining sport to engage with the social sciences in exploring the extension of the term sport in common usage. In this paper I present the results of a small survey about attitudes to sport, and use it to illustrate how a core-periphery definition of sport would proceed. (shrink)

At the heart of ethics reside the concepts of good and bad; they are at work when we assess whether a person is virtuous or vicious, an act right or wrong, a decision defensible or indefensible, a goal desirable or undesirable. But there are many varieties of goodness and badness. At their core lie intrinsic goodness and badness, the sort of value that something has for its own sake. It is in virtue of intrinsic value that other types of value (...) may be understood, and hence that we can begin to come to terms with questions of virtue and vice, right and wrong, and so on. This book investigates the nature of intrinsic value: just what it is for something to be valuable for its own sake, just what sort of thing can have such value, just how such a value is to be computed. In the final chapter, the fruits of this investigation are applied to a discussion of pleasure, pain, and displeasure and also of moral virtue and vice, in order to determine just what value lies within these phenomena. (shrink)

In this paper I explore Phyllis Rooney’s 2003 chapter, “Feminist Epistemology and Naturalized Epistemology: An Uneasy Alliance,” taking guidance from her critique of naturalized epistemology in pursuing my own analysis of another uneasy alliance: that between feminist epistemology and social epistemology. Investigating some of the background assumptions at work in prominent conceptions of social epistemology, I consider recent analyses of "epistemic bubbles" to ask how closely such analyses are aligned with ongoing research in feminist epistemology. I argue that critical feminist (...) insights in political philosophy are called for here, especially those that focus on multiple politically salient relationships and also emphasize practices of personal transformation as inseparably bound up with broader movements for social transformation. Insofar as feminist epistemology continues to carry another world in its heart, I argue that it will continue to rest uneasily with any effort to align it with—let alone subsume it within—the still emerging field of social epistemology. (shrink)

While philosophers hold that it is patently absurd to blame robots or hold them morally responsible [1], a series of recent empirical studies suggest that people do ascribe blame to AI systems and robots in certain contexts [2]. This is disconcerting: Blame might be shifted from the owners, users or designers of AI systems to the systems themselves, leading to the diminished accountability of the responsible human agents [3]. In this paper, we explore one of the potential underlying reasons for (...) robot blame, namely the folk's willingness to ascribe inculpating mental states or "mens rea" to robots. In a vignette-based experiment (N=513), we presented participants with a situation in which an agent knowingly runs the risk of bringing about substantial harm. We manipulated agent type (human v. group agent v. AI-driven robot) and outcome (neutral v. bad), and measured both moral judgment (wrongness of the action and blameworthiness of the agent) and mental states attributed to the agent (recklessness and the desire to inflict harm). We found that (i) judgments of wrongness and blame were relatively similar across agent types, possibly because (ii) attributions of mental states were, as suspected, similar across agent types. This raised the question - also explored in the experiment - whether people attribute knowledge and desire to robots in a merely metaphorical way (e.g., the robot "knew" rather than really knew). However, (iii), according to our data people were unwilling to downgrade to mens rea in a merely metaphorical sense when given the chance. Finally, (iv), we report a surprising and novel finding, which we call the inverse outcome effect on robot blame: People were less willing to blame artificial agents for bad outcomes than for neutral outcomes. This suggests that they are implicitly aware of the dangers of overattributing blame to robots when harm comes to pass, such as inappropriately letting the responsible human agent off the moral hook. (shrink)

Time may be infinite in both directions. If it is, then, if persons could live at most once in all of time, the probability that you would be alive now would be zero. But if persons can live more than once, the probability that you would be alive now would be nonzero. Since you are alive now, with certainty, either the past is finite, or persons can live more than once.

This volume presents a selection of the most influential recent discussions of the crucial metaphysical questions: what is it for one event to cause another? The subject of causation bears on many topics, such as time, explanation, mental states, the laws of nature, and the philosphy of science.

Can an ugly experiment be a good experiment? Philosophers have identified many beautiful experiments and explored ways in which their beauty might be connected to their epistemic value. In contrast, the present chapter seeks out (and celebrates) ugly experiments. Among the ugliest are those being designed by AI algorithms. Interestingly, in the contexts where such experiments tend to be deployed, low aesthetic value correlates with high epistemic value. In other words, ugly experiments can be good. Given this, we should conclude (...) that beauty is not generally necessary or sufficient for epistemic value, and increasing beauty will not generally tend to increase epistemic value. (shrink)

Using an approach deeply informed by philosophy of art, art history and perceptual psychology, this book places seeing at the centre of an original theory of pictorial representation and explores the ramifications such a theory has for the visual arts.

Basic Formal Ontology (BFO) is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined classes, and relations employing the (...) BFO framework. We provide discussion of these cases to provide a template for other ontologists using BFO, as well as to facilitate comparison with the strategies proposed by ontologists using different top-level ontologies. (shrink)

Begins by explaining then proving a generalized language dependence result similar to Goodman's "grue" problem. I then use this result to cast doubt on the existence of an objective evidential favoring relation (such as "the evidence confirms one hypothesis over another," "the evidence provides more reason to believe one hypothesis over the other," "the evidence justifies one hypothesis over the other," etc.). Once we understand what language dependence tells us about evidential favoring, our options are an implausibly strong conception of (...) the a priori, a hard externalism on which agents are unable to determine what their evidence favors, or a subjectivist view that makes evidential favoring relative to features of the agent. (shrink)

This commentary on Philip Kitcher’s book What’s the Use of Philosophy? addresses two questions. First, must philosophers be methodologically self-conscious to do good work? Second, is there value in the questions pursued in the traditional areas of analytic philosophy?

Chapter 1 addresses some preliminary issues that it is important to think about in formulating arguments from evil. Chapter 2 is then concerned with the question of how an incompatibility argument from evil is best formulated, and with possible responses to such arguments. Chapter 3 then focuses on skeptical theism, and on the work that skeptical theists need to do if they are to defend their claim of having defeated incompatibility versions of the argument from evil. Finally, Chapter 4 discusses (...) evidential arguments from evil, and four different kinds of evidential argument are set out and critically examined. (shrink)