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Barry Smith [383]Barry C. Smith [42]Barbara Herrnstein Smith [28]B. Smith [26]
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Profile: Barry Smith (State University of New York, Buffalo, National Center for Ontological Research)
Profile: Brian Cantwell Smith (University of Toronto)
Profile: Barry C Smith (School of Advanced Study, University of London)
Profile: Brian L Smith (Iona College)
Profile: Basil Smith (Saddleback College)
Profile: Ben Smith
Profile: Ben Smith (London School of Economics)
Profile: Benjamin Smith (University of Warwick)
Profile: Beth Smith (Lincoln University)
Profile: Bill Smith
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  1. Robert Arp, Barry Smith & Andrew Spear (forthcoming). Building Ontologies with Basic Formal Ontology. MIT Press, August 7, 2015.
    In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...)
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  2. B. Smith (forthcoming). Ontology and Information Science. Stanford Encyclopedia of Philosophy.
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  3. B. Smith (forthcoming). The Discovery and Development of Dolphin-Assisted Therapy. Between Species: Celebrating the Dolphin-Human Bond. Sierra Club Books, San Francisco.
     
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  4. B. C. Smith (forthcoming). Who is on Third? Subjectivity and the Physical Basis of Consciousness. Journal of Consciousness Studies.
     
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  5. Barry C. Smith (forthcoming). The Nature of Linguistic Reality: A Response to Devitt's 'Dodging'. Croatian Journal of Philosophy.
     
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  6. Bob Smith (forthcoming). Undergraduate Research Journal. Inquiry.
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  7. Brett W. Smith (forthcoming). Complex Authorial Intention in Augustine's Hermeneutics in Advance. Augustinian Studies.
  8. Werner Ceusters & Barry Smith (2015). Biomarkers in the Ontology for General Medical Science. In Ronald Cornet (ed.), Digital Healthcare Empowering Europeans. IOS Press. 155-159.
    Based on the Ontology for General Medical Science, we propose definitions for biomarkers of various types of. These definitions provide not only a complete formal representation of what biomarkers are according to the Institute of Medicine (IOM), but also remove the ambiguities and inconsistencies encountered in the documentation provided by the IOM.
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  9. Andrew R. Deans, Barry Smith & Others (2015). Finding Our Way Through Phenotypes. PLoS Biology 13 (1).
    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 (...)
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  10. Barry Smith (2015). Values in Contexts: An Ontological Theory. In G. John M. Abbarno (ed.), Inherent and Instrumental Values. Excursions in Value Inquiry. University Press of America. 17-29.
    Values exist not in isolation, but in complex wholes. Values are what they are because of the complex wholes in which they are situated. To do justice to this thesis will require a holistic ontology, a theory according to which many types of entities exist only as inseparable parts or moments of wider contexts or environments. An ontological theory of environments -- with roots in Gestalt psychology and the ecological psychology of J. J. Gibson and Roger Barker, and which is (...)
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  11. Barry Smith, Sivaram Arabandi, Mathias Brochhausen, Michael Calhoun, Paolo Ciccarese, Scott Doyle, Bernard Gibaud, Ilya Goldberg, Charles E. Kahn Jr, , James Overton, John Tomaszewski & Metin Gurcan (2015). Biomedical Imaging Ontologies: A Survey and Proposal for Future Work. Journal of Pathology Informatics 6 (37).
    Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...)
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  12. Benjamin Smith (2015). The Semiotics and Politics of “Real Selfhood” in the American Therapeutic Discourse of the World War II Era. Semiotica 2015 (203):203-226.
    Name der Zeitschrift: Semiotica Jahrgang: 2015 Heft: 203 Seiten: 203-226.
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  13. Yongqun He, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao & Barry Smith (2014). OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics 5 (29).
    A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...)
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  14. David Koepsell & Barry Smith (2014). Beyond Paper. The Monist 97 (2):222–235.
    The authors outline the way in which documents as social objects have evolved from their earliest forms to the electronic documents of the present day. They note that while certain features have remained consistent, processes regarding document authentication are seriously complicated by the easy reproducibility of digital entities. The authors argue that electronic documents also raise significant questions concerning the theory of ‘documentality’ advanced by Maurizio Ferraris, especially given the fact that interactive documents seem to blur the distinctions between the (...)
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  15. Carolyn Korsmeyer & Barry Smith (2014). Comment: Kolnai's Disgust. Emotion Review 6 (3):219-220.
    In The Meaning of Disgust, Colin McGinn employs elements of the phenomenological theory of disgust advanced by Aurel Kolnai in 1929. Kolnai’s treatment of what he calls “material” disgust and of its primary elicitors—putrefying organic matter, bodily wastes and secretions, sticky contaminants, vermin—anticipates more recent scientific treatments of this emotion as a mode of protective recoil. While Nina Strohminger charges McGinn with neglecting such scientific studies, we here attempt to show how Kolnai goes beyond experimental findings in his careful description (...)
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  16. Neil Otte, Brian Donohue & Barry Smith (2014). An Ontological Approach to Territorial Disputes. In Semantic Technology in Intelligence, Defense and Security, CEUR, vol. 1304. CEUR. 2-9.
    Disputes over territory are a major contributing factor to the disruption of international relations. We believe that a cumulative, integrated, and continuously updated resource providing information about such disputes in an easily accessible form would be of benefit to intelligence analysts, military strategists, political scientists, and also to historians and others concerned with international disputes. We propose an ontology-based strategy for creating such a resource. The resource will contain information about territorial disputes, arguments for and against claims pertaining to sovereignty, (...)
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  17. Neil Otte, Brian Donohue & Barry Smith (2014). Semantic Technology in Intelligence, Defense and Security, CEUR, Vol. 1304. CEUR.
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  18. Selja Seppälä, Barry Smith & Werner Ceusters (2014). Applying the Realism-Based Ontology-Versioning Method for Tracking Changes in the Basic Formal Ontology. In P. Garbacz & O. Kutz (eds.), Formal Ontology in Information Systems (FOIS 2014). IOS Press. 227-240.
    Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) and Evolutionary Terminology Auditing (ETA). We describe (...)
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  19. B. H. Smith (2014). An Inquiry Into Modes of Existence: An Anthropology of the Moderns. Common Knowledge 20 (3):491-493.
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  20. Barbara Herrnstein Smith (2014). Review of Bruno Latour, *An Inquiry Into Modes of Existence". [REVIEW] Common Knowledge 20 (3):491-493.
     
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  21. Barry Smith (2014). Document Acts. In Anita Konzelmann-Ziv & Hans Bernhard Schmid (eds.), Institutions, Emotions, and Group Agents. Contributions to Social Ontology. Springer. 19-31.
    The theory of document acts is an extension of the more traditional theory of speech acts advanced by Austin and Searle. It is designed to do justice to the ways in which documents can be used to bring about a variety of effects in virtue of the fact that, where speech is evanescent, documents are continuant entities. This means that documents can be preserved in such a way that they can be inspected and modified at successive points in time and (...)
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  22. Barry Smith (2014). The Relevance of Philosophical Ontology to Information and Computer Science. In Ruth Hagengruber & Uwe Riss (eds.), Philosophy, Computing and Information Science. Chatto and Pickering. 75-83.
    The discipline of ontology has enjoyed a checkered history since 1606, with a significant expansion in recent years. We focus here on those developments in the recent history of philosophy which are most relevant to the understanding of the increased acceptance of ontology, and especially of realist ontology, as a valuable method also outside the discipline of philosophy.
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  23. Barry C. Smith (2014). What Does Metacognition Do For Us? Philosophy and Phenomenological Research 89 (3):727-735.
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  24. Erik Thomsen, Fred Read, William Duncan, Tatiana Malyuta & Barry Smith (2014). Ontological Support for Living Plan Specification, Execution and Evaluation. In Semantic Technology in Intelligence, Defense and Security (STIDS). 10-17.
    Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force Research Laboratory (...)
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  25. Erik Thomsen, Fred Read, William Duncan, Tatiana Malyuta & Barry Smith (2014). Semantic Technology in Intelligence, Defense and Security (STIDS).
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  26. Ramona L. Walls, Barry Smith & Others (2014). Semantics in Support of Biodiversity: An Introduction to the Biological Collections Ontology and Related Ontologies. PLoS ONE 10.
    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...)
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  27. Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J. Mungall & Suzanna E. Lewis (2013). The Environment Ontology: Contextualising Biological and Biomedical Entities. Journal of Biomedical Semantics 4 (43).
    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; www.environmentontology.org) 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 (...)
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  28. Laurel Cooper, Ramona Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson & Barry Smith (2013). The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses. Plant and Cell Physiology 54:1-23..
    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...)
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  29. Georg Fuellen, Melanie Börries, Hauke Busch, Aubrey de Grey, Udo Hahn, Thomas Hiller, Andreas Hoeflich, Ludger Jansen, Georges E. Janssens, Christoph Kaleta, Anne C. Meinema, Sascha Schäuble, Paul N. Schofield, Barry Smith & Daniel Wuttke (2013). In-Silico-Approaches and the Role of Ontologies in Aging Research. Rejuvenation Research 16 (6):540-546.
    The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...)
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  30. Andrew Higgins & Brittany Smith, A Citation Based View of the Ontology Community in Philosophy. Proceedings of the ACM Web Science 2013.
    While many bibliometric techniques have been employed to represent the structure of academic research communities over the years, much of this work has been conducted on scientific fields as opposed to those in the humanities. Here we use graphing techniques to present two networks that allow us to explore the structure of a subset of the philosophy community by mapping the citations between philosophical texts on the topic of ontology (the study of what exists). We find a citation gap between (...)
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  31. Mark Jensen, Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule Ray, William Duncan, Patrick, Bianca Weinstock-Guttman, Barry Smith, Alan Ruttenberg, Kinga Szigeti & Alexander D. Diehl (2013). The Neurological Disease Ontology. Journal of Biomedical Semantics 4 (42).
    We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...)
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  32. Stephen B. Kennedy, Sherry Nolen, Zhenfeng Pan, Betty Smith, Jeffrey Applewhite & Kenneth J. Vanderhoff (2013). Effectiveness of a Brief Condom Promotion Program in Reducing Risky Sexual Behaviours Among African American Men. Journal of Evaluation in Clinical Practice 19 (2):408-413.
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  33. Barry Smith (2013). Diagrams, Documents, and the Meshing of Plans. In Andras Benedek & Kristof Nyiri (eds.), How To Do Things With Pictures: Skill, Practice, Performance. Peter Lang Edition.
    There are two important ways in which, when dealing with documents, we go beyond the boundaries of linear text. First, by incorporating diagrams into documents, and second, by creating complexes of intermeshed documents which may be extended in space and evolve and grow through time. The thesis of this paper is that such aggregations of documents are today indispensable to practically all complex human achievements from law and finance to orchestral performance and organized warfare. Documents provide for what we can (...)
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  34. Barry Smith (2013). Il significato della vita: come valurare una civiltà. In Philippe Nemo & Jean Petitot (eds.), Storia del liberalismo in Europa. Rubbettino. 1225-1234.
    In what respects is Western civilization superior or inferior to its rivals? In raising this question we are addressing a particularly strong form of the problem of relativism. For in order to compare civilizations one with another we would need to be in possession of a framework based on principles of evaluation which would be acceptable, in principle, to all human beings. Morality will surely provide one axis of such a framework (and we note in passing that believers in Islam (...)
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  35. Barry Smith (2013). Johanssonian Investigations. Essays in Honour of Ingvar Johansson on His Seventieth Birthday. Ontos Verlag.
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  36. Barry C. Smith (2013). L6 Philosophical and Empirical Approaches Tolanguage. In Matthew C. Haug (ed.), Philosophical Methodology: The Armchair or the Laboratory? Routledge. 294.
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  37. Barry Smith, Tatiana Malyuta, Ron Rudnicki, William Mandrick, David Salmen, Peter Morosoff, Danielle K. Duff, James Schoening & Kesny Parent (2013). IAO-Intel: An Ontology of Information Artifacts in the Intelligence Domain. CEUR 1097:33-40.
    We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata registries, (...)
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  38. Barry Smith, Lowell Vizenor & Werner Ceusters (2013). Human Action in the Healthcare Domain: A Critical Analysis of HL7’s Reference Information Model. In Johanssonian Investigations. Essays in Honour of Ingvar Johansson on His Seventieth Birthday. Ontos Verlag.
    If we are to develop efficient, reliable and secure means for sharing information across healthcare systems and organizations, then a careful analysis of human actions will be needed. To address this need, the HL7 organization has proposed its Reference Information Model (RIM), which is designed to provide a comprehensive representation of the entire domain of healthcare centered around the phenomenon of human action. Taking the Basic Formal Ontology as our starting point, we examine the RIM from an ontological point of (...)
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  39. Basil Smith (2013). Epistemology, by Ian Evans and Nicholas Smith. [REVIEW] Teaching Philosophy 36 (2):204-209.
  40. Basil Smith, Internalism and Externalism in the Philosophy of Mind and Language. Internet Encyclopedia of Philosophy.
    How are the contents of our beliefs, our intentions, and other attitudes individuated? Just what makes our contents what they are? Content externalism, as Hilary Putnam, Tyler Burge, and others have argued, is the position that our contents depend in a constitutive manner on items in the external world, that they can be individuated by our causal interaction with the items they are about. Content internalism, by contrast, is the position that our contents depend primarily on the properties of our (...)
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  41. Basil Smith (2013). Knowledge," by Ian Evans and Nicholas Smith. [REVIEW] Teaching Philosophy 36 (2):204-209.
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  42. Benedict Smith (2013). Depression and Motivation. Phenomenology and the Cognitive Sciences 12 (4):615-635.
    Among the characteristic features of depression is a diminishment in or lack of action and motivation. In this paper, I consider a dominant philosophical account which purports to explain this lack of action or motivation. This approach comes in different versions but a common theme is, I argue, an over reliance on psychologistic assumptions about action–explanation and the nature of motivation. As a corrective I consider an alternative view that gives a prominent place to the body in motivation. Central to (...)
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  43. Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith (2012). Representing Mental Functioning: Ontologies for Mental Health and Disease. In Towards an Ontology of Mental Functioning (ICBO Workshop), Proceeedings of the Third International Conference on Biomedical Ontology.
    Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...)
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  44. Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith (2012). Towards an Ontology of Mental Functioning (ICBO Workshop), Proceeedings of the Third International Conference on Biomedical Ontology.
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  45. Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan & Barry Smith (2012). Wanting What We Don't Want to Want: Representing Addiction in Interoperable Bio-Ontologies. In Ronald Cornet & Robert Stevens (eds.), Proceeedings of the Third International Conference on Biomedical Ontology. CEUR. 56-60.
    Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...)
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  46. Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan & Barry Smith (2012). Proceeedings of the Third International Conference on Biomedical Ontology. CEUR.
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  47. Mark A. Musen, Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, Margaret-Anne Story & Barry Smith (2012). The National Center for Biomedical Ontology. Journal of the American Medical Informatics Association 19 (2):190-195.
    The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...)
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  48. Barbara Herrnstein Smith (2012). Cognitively Unnatural Science? In Simen Andersen Øyen & Tone Lund-Olsen (eds.), Sacred Science?: On Science and its Interrelations with Religious Worldviews. Wageningen Academic Publishers.
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  49. Barry Smith (2012). Classifying Processes: An Essay in Applied Ontology. Ratio 25 (4):463-488.
    We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within a single framework. We (...)
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  50. Barry Smith (2012). How to Do Things with Documents. Rivista di Estetica 50 (50):179-198.
    This essay is a contribution to social ontology, drawing on the work of John Searle and of Hernando de Soto. At the center of the argument is the proposition advanced by de Soto in his Mystery of Capital to the effect that many of the entities which structure our contemporary social reality are entities which exist in virtue of the fact that there are (paper or digital) documents which support their existence. I here develop de Soto’s argument further, focusing specifically (...)
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