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)
This essay criticizes the proposal recently defended by a number of prominent economists that welfare economics be redirected away from the satisfaction of people's preferences and toward making people happy instead. Although information about happiness may sometimes be of use, the notion of happiness is sufficiently ambiguous and the objections to identifying welfare with happiness are sufficiently serious that welfare economists are better off using preference satisfaction as a measure of welfare. The essay also examines and criticizes the position associated (...) with Daniel Kahneman and a number of co-authors that takes welfare to be ‘objective happiness’ – that is, the sum of momentary pleasures. (shrink)
Many libertarians believe that self-ownership is a separate matter from ownership of extra-personal property. “No-proviso” libertarians hold that property ownership should be free of any “fair share” constraints, on the grounds that the inability of the very poor to control property leaves their self-ownership intact. By contrast, left-libertarians hold that while no one need compensate others for owning himself, still property owners must compensate others for owning extra-personal property. What would a “self” have to be for these claims to be (...) true? I argue that both of these camps must conceive of the boundaries of the self as including one's body but no part of the extra-personal world. However, other libertarians draw those boundaries differently, so that self-ownership cannot be separated from the right to control extra-personal property after all. In that case, property ownership must be subject to a fair share constraint, but that constraint does not require appropriators to pay compensation. This view, which I call “right libertarianism,” differs importantly from the other types primarily in its conception of the self, which I argue is independently more plausible. (shrink)
Conversational partners' representations may be less aligned than they appear even when interlocutors believe they have successfully understood each other, as data from a series of experiments on surveys about facts and behaviors suggest. Although the goal of a mechanistic psychology of dialogue is laudable, the ultimate model is likely to require far greater specification of individual and contextual variability.
The tenuous claims of cost-benefit analysis to guide policy so as to promote welfare turn on measuring welfare by preference satisfaction and taking willingness-to-pay to indicate preferences. Yet it is obvious that people's preferences are not always self-interested and that false beliefs may lead people to prefer what is worse for them even when people are self-interested. So welfare is not preference satisfaction, and hence it appears that cost-benefit analysis and welfare economics in general rely on a mistaken theory of (...) well-being. This essay explores the difficulties, criticizes standard defences of welfare economics, and then offers a new partial defence that maintains that welfare economics is independent of any philosophical theory of well-being. Welfare economics requires nothing more than an evidential connection between preference and welfare: in circumstances in which people are concerned with their own interests and reasonably good judges of what will serve their interests, their preferences will be reliable indicators of what is good for them. (shrink)
This essay attempts to distinguish the pressing issues for economists and economic methodologists concerning realism in economics from those issues that are of comparatively slight importance. In particular I shall argue that issues concerning the goals of science are of considerable interest in economics, unlike issues concerning the evidence for claims about unobservables, which have comparatively little relevance. In making this argument, this essay raises doubts about the two programs in contemporary economic methodology that raise the banner of realism. In (...) particular I argue that the banner makes it more difficult to relate the concerns of those who wave it to those of other methodologists. Although this essay argues that many of the debates in this century between scientific realists and their opponents are not relevant to economics, it does not attack scientific realism, and it does not urge economists or economic methodologists to reject it. (shrink)
The psychological condition of happiness is normally considered a paradigm subjective good, and is closely associated with subjectivist accounts of well-being. This article argues that the value of happiness is best accounted for by a non-subjectivist approach to welfare: a eudaimonistic account that grounds well-being in the fulfillment of our natures, specifically in self-fulfillment. And self-fulfillment consists partly in authentic happiness. A major reason for this is that happiness, conceived in terms of emotional state, bears a special relationship to the (...) self. These arguments also point to a more sentimentalist approach to well-being than one finds in most contemporary accounts, particularly among Aristotelian forms of eudaimonism. (shrink)
Childhood overweight and obesity, especially among migrant children, are current health problems in several European countries. In the present study the prevalence of overweight and obesity among migrant children from Turkey and the former Yugoslavia was documented and compared with that of Austrian children in Vienna. Anthropometric data from 1786 children were collected at the ages of 6, 10 and 15 years. Body mass was estimated by means of the body mass index and percentile curves were used to determine weight (...) status. The prevalence of overweight and obesity was found to be significantly higher among migrant children. Children and adolescents from the former Yugoslavia and Turkish girls exhibited especially high rates of overweight and obesity. Biosocial and cultural factors are discussed as causes of these observations. (shrink)
In the Groundwork of the Metaphysic of Morals' Kant is explicit, sometimes to the point of peevishness, in denying anthropology and psychology any part or place in his moral science. Recognizing that this will strike many as counterintuitive he is unrepentant: ‘We require no skill to make ourselves intelligible to the multitude once we renounce all profundity of thought’. That the doctrine to be defended is not exemplified in daily experience or even in imaginable encounters is necessitated by the very (...) nature of morality which cannot be served worse ‘… than by seeking to derive it from examples’. Thus, the project of the moral philosopher begins with the recognition that the moral realm is not mapped by anthropological data and does not get its content therefrom. Rather, moral philosophy must be ‘completely cleansed’ of everything that is appropriate to anthropology. (shrink)
In this book Daniel Wegner offers a novel understanding of the relation of consciousness, the will, and our intentional and voluntary actions. Wegner claims that our experience and common sense view according to which we can influence our behavior roughly the way we experience that we do it is an illusion.
It is extraordinary, when one thinks about it, how little attention has been paid by theorists of the nature and justification of punishment to the idea that punishment is essentially a matter of self-defense. H. L. A. Hart, for example, in his famous “Prolegomenon to the Principles of Punishment,” is clearly committed to the view that, at bottom, there are just three directions in which a plausible theory of punishment can go: we can try to justify punishment on purely consequentialist (...) grounds, which for Hart, I think, would be to try to construct a purely utilitarian justification of punishment; we can try to justify punishment on purely retributive grounds; or we can try to justify punishment on grounds that are some sort of shrewd combination of consequentialist and retributive considerations. Entirely absent from Hart's discussion is any consideration of the possibility that punishment might be neither a matter of maximizing the good, nor of exacting retribution for a wrongful act, nor of some imaginative combination of these things, but, rather, of something altogether different from either of them: namely, the exercise of a fundamental right of self-protection. Similarly, but much more recently, R. A. Duff, despite the fact that he himself introduces and defends an extremely interesting fourth possibility, begins his discussion by writing as though, apart from his contribution, there are available to us essentially just the options previously sketched by Hart. Again, there is no mention here, any more than in Hart's or any number of other recent discussions, of the possibility that we might be able to justify the institution of punishment on grounds that are indeed forward-looking, to use Hart's famous term, but that are not at all consequentialist in any ordinary sense of the word. (shrink)
By embodying the hopes of a set of qualitative liberals who believed that postwar economic abundance opened up opportunities for self-development, David Riesman's bestselling The Lonely Crowd influenced the New Left. Yet Riesman's assessment of radical youth protest shifted over the course of the 1960s. As an antinuclear activist he worked closely with New Left leaders during the early 1960s. By the end of the decade, he became a sharp critic of radical protest. However, other leading members of Riesman's circle, (...) such as Kenneth Keniston, author of the influential Young Radicals, applied Riesman's ideas to create more sympathetic understandings of the New Left. Examining reactions to the New Left by Riesman and his associates allows historians to go beyond the common understanding of the key ideological divisions of the 1960s as existing between liberalism and radicalism or between liberalism and conservatism to better appreciate the significance of splits among liberals themselves. (shrink)
In this paper on Karl Barth's conception of truth I shall try to state his position regarding the nature of truth and the criterion of truth, and secondly I shall draw from his position some propositions which I believe exhibit a pattern in his theology which brings it into close relationship to a philosophical tradition.
Physicalism, the thesis that everything is physical, is one of the most controversial problems in philosophy. Its adherents argue that there is no more important doctrine in philosophy, whilst its opponents claim that its role is greatly exaggerated. In this superb introduction to the problem Daniel Stoljar focuses on three fundamental questions: the interpretation, truth and philosophical significance of physicalism. In answering these questions he covers the following key topics: -/- (i)A brief history of physicalism and its definitions, (ii)what (...) a physical property is and how physicalism meets challenges from empirical sciences, (iii)'Hempel’s dilemma’ and the relationship between physicalism and physics, (iv)physicalism and key debates in metaphysics and philosophy of mind, such as supervenience, identity and conceivability, and (v)physicalism and causality. -/- Additional features include chapter summaries, annotated further reading and a glossary of technical terms, making Physicalism ideal for those coming to the problem for the first time. (shrink)