The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (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)

The development of symbolic logic is often presented in terms of a cumulative story of consecutive innovations that led to what is known as modern logic. This narrative hides the difficulties that this new logic faced at first, which shaped its history. Indeed, negative reactions to the emergence of the new logic in the second half of the nineteenth century were numerous and we study here one case, namely logic at Oxford, where one finds Lewis Carroll, a mathematical teacher (...) who promoted symbolic logic, and John Cook Wilson, the Wykeham Professor of Logic who notoriously opposed it. An analysis of their disputes on the topic of logical symbolism shows that their opposition was not as sharp as it might look at first, as Cook Wilson was not so much opposed to the « symbolic » character of logic, but the intrusion of mathematics and what he perceived to be the futility of some of its problems, for logicians and philosophers alike. (shrink)

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)

Smith proposes an account of how languages developed. He did so not as historian, but as a philosopher with a special concern about how a nominalist could account for general terms. Names for individuals are taken as fairly unproblematic – say ‘Thames’ and ‘Avon’ for each of the respective rivers. But whence the word ‘river,’ applicable to more than one, if all that exist are particular objects? Smith’s view is not the usual one, according to which people deploy (...) a powerful ability to abstract mentally, and subsequently affix a label to a general concept. He resisted this because he granted that such robust mental processes themselves presuppose the use of words. Rather, what holds the class together is the word itself, a “single appellation.”. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (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)

Recently, the practice of deciding legal cases on purely statistical evidence has been widely criticised. Many feel uncomfortable with finding someone guilty on the basis of bare probabilities, even though the chance of error might be stupendously small. This is an important issue: with the rise of DNA profiling, courts are increasingly faced with purely statistical evidence. A prominent line of argument—endorsed by Blome-Tillmann 2017; Smith 2018; and Littlejohn 2018—rejects the use of such evidence by appealing to epistemic norms (...) that apply to individual inquirers. My aim in this paper is to rehabilitate purely statistical evidence by arguing that, given the broader aims of legal systems, there are scenarios in which relying on such evidence is appropriate. Along the way I explain why popular arguments appealing to individual epistemic norms to reject legal reliance on bare statistics are unconvincing, by showing that courts and individuals face different epistemic predicaments (in short, individuals can hedge when confronted with statistical evidence, whilst legal tribunals cannot). I also correct some misconceptions about legal practice that have found their way into the recent literature. (shrink)

I distinguish paradoxes and hypodoxes among the conundrums of time travel. I introduce ‘hypodoxes’ as a term for seemingly consistent conundrums that seem to be related to various paradoxes, as the Truth-teller is related to the Liar. In this article, I briefly compare paradoxes and hypodoxes of time travel with Liar paradoxes and Truth-teller hypodoxes. I also discuss Lewis’ treatment of time travel paradoxes, which I characterise as a Laissez Faire theory of time travel. Time travel paradoxes are impossible (...) according to Laissez Faire theories, while it seems hypodoxes are possible. (shrink)

Entitlement is conceived as a kind of positive epistemic status, attaching to certain propositions, that involves no cognitive or intellectual accomplishment on the part of the beneficiary — a status that is in place by default. In this paper I will argue that the notion of entitlement — or something very like it — falls out of an idea that may at first blush seem rather disparate: that the evidential support relation can be understood as a kind of variably strict (...) conditional (in the sense of Lewis 1973). Lewis provided a general recipe for deriving what he termed inner modalities from any variably strict conditional governed by a logic meeting certain constraints. On my proposal, entitlement need be nothing more exotic than the inner necessity associated with evidential support. Understanding entitlement in this way helps to answer some common concerns — in particular, the concern that entitlement could only be a pragmatic, and not genuinely epistemic, status. (shrink)

We present a dynamic model of the evolution of communication in a Lewis signaling game while systematically varying the degree of common interest between sender and receiver. We show that the level of common interest between sender and receiver is strongly predictive of the amount of information transferred between them. We also discuss a set of rare but interesting cases in which common interest is almost entirely absent, yet substantial information transfer persists in a *cheap talk* regime, and offer (...) a diagnosis of how this may arise. -/- . (shrink)

This volume brings together a range of influential essays by distinguished philosophers and political theorists on the issue of global justice. Global justice concerns the search for ethical norms that should govern interactions between people, states, corporations and other agents acting in the global arena, as well as the design of social institutions that link them together. The volume includes articles that engage with major theoretical questions such as the applicability of the ideals of social and economic equality to the (...) global sphere, the degree of justified partiality to compatriots, and the nature and extent of the responsibilities of the affluent to address global poverty and other hardships abroad. It also features articles that bring the theoretical insights of global justice thinkers to bear on matters of practical concern to contemporary societies, such policies associated with immigration, international trade, and climate change. -/- Contents: Introduction; Part I Standards of Global Justice: (i) Assistance-Based Responsibilities to the Global Poor: Famine, affluence and mortality, Peter Singer; We don't owe them a thing! A tough-minded but soft-hearted view of aid to the faraway needy, Jan Narveson; Does distance matter morally to the duty to rescue? Frances Myrna Kamm. (ii) Contribution-Based Responsibilities to the Global Poor: 'Assisting' the global poor, Thomas Pogge; Should we stop thinking about poverty in terms of helping the poor?, Alan Patten; Poverty and the moral significance of contribution, Gerhard Øverland. (iii)Cosmopolitans, Global Egalitarians, and its Critics: The one and the many faces of cosmopolitanism, Catherine Lu; Cosmopolitan justice and equalizing opportunities, Simon Caney; The problem of global justice, Thomas Nagel; Against global egalitarianism, David Miller; Egalitarian challenges to global egalitarianism: a critique, Christian Barry and Laura Valentini. Part II Pressing Global Socioeconomic Issues: (i) Governing the Flow of People: Immigration and freedom of association, Christopher Wellman; Democratic theory and border coercion: no right to unilaterally control your own borders, Arash Abizadeh; Justice in migration: a closed borders utopia?, Lea Ypi. (ii) Climate Change: Global environment and international inequality, Henry Shue; Valuing policies in response to climate change: some ethical issues, John Broome; Saved by disaster? Abrupt climate change, political inertia, and the possibility of an intergenerational arms race, Stephen M. Gardiner; Polycentric systems for coping with collective action and global environmental change, Elinor Ostrom. (iii) International Trade: Responsibility and global labor justice, Iris Marion Young; Property rights and the resource curse, Leif Wenar; Fairness in trade I: obligations arising from trading and the pauper-labor argument, Mathias Risse; Name index. -/- See: www.ashgate.com/default.aspx?page=637&calctitle=1&pageSubject=483&sort=pubdate&forthcoming=1&title_i d=9958&edition_id=13385. (shrink)

What is the concept of sense developed by Deleuze in his 1969 Logic of Sense? This paper attempts to answer this question analysing the three dimensions of language that Deleuze isolates: the primary order of noises and intensities ; the secondary order of sense ; and the tertiary organisation of propositions. What renders language possible is that which separates sounds from bodies and organises them into propositions, freeing them for the expressive function. Deleuze argues that it is the dimension of (...) sense that brings about this genesis of language, and he analyses in detail the three syntheses that bring about the production of this surface of sense. Yet Deleuze also distinguishes between two types of non-sense: the nonsense of Lewis Carroll's portmanteau words, which remain ensconced in the dimension of sense, and the more profound nonsense of Antonin Artaud's psychotic scream-breaths, which penetrate the almost unbearable world of the primary order of noise and intensities. In the end, the focus of Logic of Sense is less the surface domain of sense than the primary depth of corporeal intensities. What Deleuze calls a ‘minor’ use of language is nothing other than an intensive use of language that constitutes a principle of metamorphosis. (shrink)

The ethos of Justin Smith’s Nature, Human Nature, & Human Difference is expressed in the narrative of Anton Wilhelm Amo (~1703-53), an African-born​ slave who earned his doctoral degree in Philosophy at a European university and went on to teach at the Universities of Jena and Halle. Smith identifies Amo as a time-marker for diverging interpretations of race: race as inherently tethered to physical difference and race as inherited essential difference. Further, these interpretations of race are fastened to (...) the discourse of science and human diversity within modern Europe. Smith’s thesis maintains that the rise of the concept of race in philosophy begins with a divorcing of the soul from human nature and a movement to a naturalistic classification of human beings through taxonomies (e.g. botany, mineralogy and zoology), which dissolved into this dichotomy: an essential difference between people of reason and people of nature. (shrink)

A critique of dubious contrasts between "science" and "religion" drawn on the basis of cognitive-evolutionary accounts of human psychology, e.g.,. the claim that religious concepts are “likely” and “natural” for the human mind whereas scientific thinking is “rare” and “unnatural.” Initially made by biologist Lewis Wolpert in *The Unnatural Nature of Science* (1993) and anthropologist Pascal Boyer in *Religion Explained: The Evolutionary Origins of Religious Thought* (2001), they are developed at length by philosopher R. N. McCauley in a*Why Religion (...) is Natural and Science is Not* (2011). These contrasts involve tendentiously narrow or broad definitions of the terms “science” and “religion” and the obliteration of the complex historical and intellectual relations between the ideas and practices currently identified by those terms. (shrink)

J. David Lewis and Richard L. Smith provide a history of pragmatism and Chicago sociology based on the positions of realism and nominalism. This issue is indeed the key to understanding pragmatism’s foundations in Charles Peirce’s original formulation. Lewis and Smith claim that there are two pragmatisms, a realistic one characterized by Peirce and Mead and a nominalistic one (which Lewis and Smith claim has no value) illustrated by James and Dewey. They argue that (...) Chicago sociology, including Herbert Blumer, was under the influence of the nominalistic pragmatism, and that Mead exercised little influence during his lifetime. The argument is based on an ahistorical, a priori "metatheoretical" realism-nominalism distinction that claims to be based on Peirce's discussions of realism and nominalism. Yet the authors support their understanding of realism by appealing to Mead’s discussion of “contact experience,” and claim that Peirce’s realism must be based in non-symbolic “pure resistance.” Ironically, such a view represents the main tenet of nominalism, that only individual particulars are real, and amounts to a denial of Peirce’s category of Thirdness as reducible to the “pure resistance” of Secondness. Lewis and Smith attempt to correct the subjectivist tendencies of symbolic interactionism yet would problematically replace them with an equally subjective view of what constitutes objectivity: individual reaction with an object. American Sociology and Pragmatism tends to present a monistic universe hinging on a nominalistic interpretation of realism, a single-visioned view that places more emphasis on labels than on the substance and pragmatic import of a theorist's thoughts, resulting in serious distortions pro and con. Yet it also has opened up for serious questioning the whole foundations of symbolic interactionism and Mead's place within pragmatism and Chicago sociology. Though the authors claim to be "revisionists," it seems to me that they are also "fundamentalists" in safely preserving Mead at the center of a history they claim he did not significantly influence. In my opinion the ongoing controversy will result in a broader understanding of the antecedents of contemporary symbolic interactionism, one that will call for Mead's now dominating role as the sole representative of pragmatism for many American sociologists to be reevaluated and placed within the context of the quite substantial contributions of Peirce, James, and Dewey. (shrink)

În această lucrare analizez posibilitatea călătoriei în timp pe baza mai multor lucrări de specialitate, printre care cele ale lui Nicholas J.J. Smith ("Time Travel", The Stanford Encyclopedia of Philosophy”), William Grey (”Troubles with Time Travel”), Ulrich Meyer (”Explaining causal loops”), Simon Keller și Michael Nelson (”Presentists should believe in time-travel”), Frank Arntzenius și Tim Maudlin ("Time Travel and Modern Physics") și David Lewis (“The Paradoxes of Time Travel”). Lucrarea începe cu o Introducere în care fac o scurtă (...) prezentare a călătoriei în timp, și continuă cu o Istoria conceptului de călătorie în timp, prezentarea principalelor Aspecte fizice ale călătoriei în timp, inclusiv călătoria în timp în trecut în relativitatea generală și în fizica cuantică și călătoria în timp în viitor, apoi o prezentare a Paradoxul bunicului care este abordat în aproape toate lucrările de specialitate, urmat de o secțiune dedicată Filosofiei călătoriei în timp, și o secțiune în care analizez Buclele cauzale pentru călătoria în timp. Finalizez lucrarea cu Concluzii, în care expun opiniile personale privind călătoria în timp, și Bibliografia pe care se bazează lucrarea. (shrink)

In this article, on the basis of analysis of the classical definition of a miracle (from D.Hume to C.S.Lewis and R. Swinburne) and the nonclassical one (J.L. Marion and J.P.Manussakis), the phenomenological and the etymological aspects of a miracle are examined.Taking into consideration the historical development of the concept of a miracle, the author proves the connections between contemplation, miracle and novelty. They are necessary for the constituting of religious experience. Faith itself, in theological sense, is not determinative (...) for religious experience.It has sense only when it is integrated into contemplation. True religious experience is based on the art of contemplation which helps a human being to look with astonishment. The author argues that phenomenological approach to a miracle combined with the etymological analysis is a valuable method for the study of a miracle in the context of the history of philosophy. (shrink)

1000 time-travelers travel back in time, each with the intention of killing their own infant-self. If there is no branching time, then on pain of bringing about a logical contradiction, all must fail. But this seems inexplicable: what is to ensure that the time-travelers are stopped? For a time, this inexplicability objection was thought to provide evidence that there is something incoherent about the possibility of backwards time travel in a universe without branching time. There is now near-consensus, however, that (...) the objection has no bite: there is nothing inexplicable about the mass failure. Lewis, Sider and Ismael independently argue that since it is built into the description of the class of cases considered that the time-travelers must fail – and so we consider only unsuccessful attempts – there is no mystery. Smith argues that the absence of possible worlds at which auto-infanticide is committed suffices as a complete explanation for the failures. And Baron and Colyvan maintain that available causal and logical explanations jointly account for everything that needs accounting for. I argue that these are wrong. There is remaining, problematic inexplicability. For backwards time travel not to lead to logical contradiction, something would need to do logic’s bidding, after all. (shrink)

About the possibility of time traveling based on several specialized works, including those of Nicholas J. J. Smith ("Time Travel"), William Grey (”Troubles with Time Travel”), Ulrich Meyer (”Explaining causal loops”), Simon Keller and Michael Nelson (”Presentists should believe in time-travel”), Frank Arntzenius and Tim Maudlin ("Time Travel and Modern Physics"), and David Lewis (“The Paradoxes of Time Travel”). The article begins with an Introduction in which I make a short presentation of the time travel, and continues with (...) a History of the concept of time travel, main physical aspects of time travel, including backward time travel in the past in general relativity and quantum physics, and time travel in the future, then a presentation of the Grandfather paradox that is approached in almost all specialized works, followed by a section dedicated to the Philosophy of time travel, and a section in which I analyze Causal loops for time travel. I finish my work with Conclusions, in which I sustain my personal opinions on the time travel, and the Bibliography on which the work is based. -/- ISSN 978-606-033-195-7, DOI: 10.58679/TW82554. (shrink)

À propos de la possibilité de voyager dans le temps sur la base de plusieurs ouvrages spécialisés, notamment ceux de Nicholas J. J. Smith (« Time Travel »), William Grey (« Troubles with Time Travel »), Ulrich Meyer (« Explaining causal loops »), Simon Keller and Michael Nelson (« Presentists should believe in time-travel »), Frank Arntzenius and Tim Maudlin (« Time Travel and Modern Physics »), et David Lewis (« The Paradoxes of Time Travel »). L'article commence (...) par une Introduction dans laquelle je fais une brève présentation du voyage dans le temps et poursuit par une Histoire du concept de voyage dans le temps, les principaux aspects physiques du voyage dans le temps, y compris les voyages dans le temps dans le passé dans la relativité générale et la physique quantique , et les voyages dans le temps dans le futur, puis une présentation du Paradoxe du grand-père abordé dans presque toutes les œuvres spécialisées, suivie d’une section consacrée à la Philosophie du voyage dans le temps et d’une section dans laquelle j’analyse les Boucles causales pour le voyage dans le temps. Je termine mon travail avec Conclusions, dans laquelle je maintiens mes opinions personnelles sur le voyage dans le temps et la Bibliographie sur laquelle repose le travail. -/- TABLE: -/- Abstract Introducere Istoria conceptului de călătorie în timp Paradoxul bunicului Filosofía călătoriei în timp Buclele cauzale Concluzii Note Bibliografie -/- DOI: 10.13140/RG.2.2.27116.51841. (shrink)

Epistemic permissivism is the view that it is possible for two people to rationally hold incompatible attitudes toward some proposition on the basis of one body of evidence. In this paper, I defend a particular version of permissivism – unacknowledged permissivism (UP) – which says that permissivism is true, but that no one can ever rationally believe that she is in a permissive case. I show that counter to what virtually all authors who have discussed UP claim, UP is an (...) attractive view: it is compatible with the intuitive motivations for permissivism and avoids a significant challenge to permissivism: the arbitrariness objection. (shrink)

Roland Greene and Stephen Cushman have revived the 1950s' edition of this book. & it is worth reading even by philosophers for in the final analysis, from Plato to Blanchot to Jean-Luc Marion are all poets. Where does poetry end and philosophy begin!!??

An interview by Alex Thomson of UKColumn on Landgrebe and Smith's book: Why Machines Will Never Rule the World. The subtitle of the book is Artificial Intelligence Without Fear, and the interview begins with the question of the supposedly imminent takeover of one profession or the other by artificial intelligence. Is there truly reason to be afraid that you will lose your job? The interview itself is titled 'Where this is no will there is no way', drawing on one (...) thesis of the book to the effect that there will never be anything like the human will on the part of a machine. This is for mathematical reasons. AI is always and in every case a matter of algorithms; thus of applied mathematics. And algorithms are not the sorts of things that can want or desire or intend to do something. It is the human will of those who work at OpenAI or google or microsoft which have given rise to the new shiny objects of AI (ChatGPT and other Large Language Models). And it is the human will of the users of these shiny objects which gives them the resources and power to work their apparent miracles. (shrink)

Several quantitative surveys have been conducted internationally to gather empirical information about physicians’ general attitudes towards health care rationing. Are physicians ready to accept and implement rationing, or are they rather reluctant? Do they prefer implicit bedside rationing that allows the physician–patient relationship broad leeway in individual decisions? Or do physicians prefer strategies that apply explicit criteria and rules?

This study establishes the influence of sex-based grammatical gender on gendered violence. We demonstrate a statistically significant relationship between gendered language and the incidence of intimate partner violence in a cross-section of countries. Motivated by this evidence, we conduct an individual-level analysis exploiting the differences in the language structures spoken by individuals with a shared religious and ethnic background residing in the same country. We show that speaking a gendered language is associated with the belief that intimate partner violence is (...) justifiable. Our results are consistent with the theoretical possibility that gendered language activates gender schemata in the minds of speakers, increasing the salience of gender distinctions and existing gender norms which legitimize gendered violence. (shrink)

As a contribution to a wider discussion on moral discernment in theological anthropology, this paper seeks to answer the question “What is the impact of mental illness on an individual’s ability to make moral decisions?” Written from a clinical psychiatric perspective, it considers recent contributions from psychology, neuropsychology and imaging technology. It notes that the popular conception that mental illness necessarily robs an individual of moral responsibility is largely unfounded. Most people who suffer from mental health problems do not lose (...) the capacity to make moral decisions, and mental illness on its own rarely explains anti-social or criminal behaviour. Moreover, the assumptions of some scientists, that recent developments in neuropsychology and brain imaging suggest biological determinism, must be treated with caution. (shrink)

The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...) Common ontologies (consensus-based controlled vocabularies) have proved themselves in various domains as a valuable tool for solving such problems. In this paper, we present a consensus-based Additive Manufacturing Ontology (AMO) and illustrate its application in promoting re-usability in the field of dentistry product manufacturing. (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds of (...) situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve the representation of contractual (...) obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (shrink)

In this paper, I argue that the two versions of divided line create problems that cannot be solved — with or without the hypothesis that the objects belonging to the level of διάνοια on the divided line are intermediates. I also argue that the discussion of arithmetic and calculation does not fit Aristotle’s attribution of intermediates to Plato and provides no support for the claim that Plato had such intermediates in mind when he talked about διάνοια in the Republic. The (...) upshot of my argument is negative: even if Aristotle’s report about Plato and intermediates is correct, there is no evidence for such objects provided in the passages I review from the Republic. If they are to be found in Plato, it will have to be elsewhere that they are found. (shrink)

The current rise of neurodevelopmental disorders poses a critical need to detect risk early in order to rapidly intervene. One of the tools pediatricians use to track development is the standard growth chart. The growth charts are somewhat limited in predicting possible neurodevelopmental issues. They rely on linear models and assumptions of normality for physical growth data – obscuring key statistical information about possible neurodevelopmental risk in growth data that actually has accelerated, non-linear rates-of-change and variability encompassing skewed distributions. Here, (...) we use new analytics to profile growth data from 36 newborn babies that were tracked longitudinally for 5 months. By switching to incremental (velocity-based) growth charts and combining these dynamic changes with underlying fluctuations in motor performance – as the transition from spontaneous random noise to a systematic signal – we demonstrate a method to detect very early stunting in the development of voluntary neuromotor control and to flag risk of neurodevelopmental derail. (shrink)

Second part of the translation into Spanish of David Lewis' "New Work for a Theory of Universals", corresponding to the last sections of the original paper. || Segunda parte de la traducción al español del trabajo de David Lewis "New Work for a Theory of Universals", correspondiente a últimas secciones del artículo original. Artículo original publicado en: Australasian Journal of Philosophy, Vol. 61, No. 4, Dec. 1983, pp. 343-377.

Provides a survey of the development of speech act theory from Aristotle through Reid and Peirce to Edmund Husserl, Anton Marty, Johannes Daubert, Adolf Reinach, and finally to Austin and Searle. A special role is played by Husserl's theory of objectifying acts (meaning, roughly, acts of naming or stating) and of the efforts by his followers to extend this theory to cover phenomena such as questioning and commanding. These efforts culminated in the work of Adolf Reinach, who developed the first (...) systematic theory of speech acts in connection with his monograph of 1913 on “The A Priori Foundations of the Civil Law”. (shrink)

We provide an overview of Searle's contributions to speech act theory and the ontology of social reality, focusing on his theory of constitutive rules. In early versions of this theory, Searle proposed that all such rules have the form 'X counts as Y in context C' formula – as for example when Barack Obama (X) counts as President of the United States (Y) in the context of US political affairs. Crucially, the X and the Y terms are here identical. A (...) problem arises for this theory for cases involving 'free-standing Y terms', as for example in the case of money in a computerized bank account. Here there is no physical X to which a status function might be attached. We conclude by arguing that Searle's response to this problem creates difficulties for his naturalistic framework. (shrink)

Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data (...) Analysis, and Resources—for data archiving, dissemination, analyses, and reuse. To date, more than 300 studies have been made freely available through the ImmPort Shared Data portal , which allows research data to be repurposed to accelerate the translation of new insights into discoveries. (shrink)

Intelligent defence support systems are confronted with the need to manage ever-increasing floods of data in a way that raises significant challenges because the data are described and presented using different terminologies and formats. How, on this basis, is it possible to reach a common understanding of the information content of these data among people and software agents? How is it possible to ensure that domain knowledge is reused in consistent fashion in a way that makes this information available for (...) integration and analysis? How can we support the identification, selection, composition, and orchestration of services based on such diverse data providing homogeneous support by a service-oriented architecture? This collection is devoted to the use of ontologies to answer questions such as these. (shrink)

Pojęcie niszy (otoczenia, kontekstu, siedliska, środowiska) nie cieszy się specjalnym zainteresowaniem ontologów, mimo że ma szerokie zastosowanie w rozmaitych dyscyplinach, od biologii ewolucyjnej po ekonomię. Niniejszy artykuł zawiera pierwszą teorię formalną tego pojęcia — teorię relacji pomiędzy przedmiotami a ich niszami. Teoria ta opiera się na istniejącym dorobku mereologii, topologii i teorii lokalizacji przestrzennej, które są narzędziami ontologii formalnej. Jest ona tutaj ilustrowana głównie za pomocą prostych przykładów z biologii, ale pojęcie niszy należy rozumieć — podobnie jak pojęcia części, granicy (...) i położenia — jako pojęcie strukturalne, znajdujące zastosowanie w obszernym zakresie różnych dziedzin. (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.

Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task remains of ensuring that the right sorts of information reach the right sorts of people. In what follows we defend the thesis that efforts to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations, and that the communication of healthcare information and knowledge needs to rest (...) on a sound ontology of social interaction. We illustrate this thesis in relation to the HL7 RIM, which is one centrally important tool for communication in the healthcare domain. (shrink)

First part of the translation into Spanish of David Lewis' "New Work for a Theory of Universals", corresponding to the introduction and the first two sections of the original paper. || Primera parte de la traducción al español del trabajo de David Lewis "New Work for a Theory of Universals", correspondiente a la introducción y las dos primeras secciones del artículo original. Artículo original publicado en: Australasian Journal of Philosophy, Vol. 61, No. 4, Dec. 1983, pp. 343-377.

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical power and (...) great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that (...) the pump exists because something was needed that would pump water. A water pump may have many capabilities, including: to be weatherproof, to run without lubricant, to be transportable, and so forth. But its function is to pump water. We focus here on capabilities possessed by humans – such as piano playing or language using – and we explore the relation between capabilities of these sorts and structures in the brain. (shrink)

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)

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and (...) maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

In the present review we focus on what we take to be some remaining issues with the Behaviour Change Intervention Ontology (BCIO). We are in full agreement with the authors’ endorsement of the principles of best practice for ontology development In particular, we agree that an ontology should be “logically consistent and having a clear structures [sic], preferably a well-organised hierarchical structure,” and that “Maximising the new ontology’s interoperability with existing ontologies by reusing entities from existing ontologies where appropriate” is (...) critically important (Wright et al., 2020, p. 17). Our remaining concerns with BCIO relate directly to these two principles. First, we identify a number of issues with some of the classifications and definitions in BCIO that seem to be in tension with the just-mentioned principle . Second, we note some reservations about the reuse of certain classes in BCIO, namely from the Gazetteer (GAZ), the Ontology of Medically Related Social Entities (OMRSE), and the Information Artifact Ontology (IAO). While the latter principle of “reuse” is important, it is also important not to let the reuse of existing classes (or their corresponding definitions) compromise the logical integrity or the realist nature of one’s ontology. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)