Results for 'Nicholas J. J. Smith'

1000+ found
Order:
See also
Nicholas J. J. Smith
University of Sydney
  1. Bioportal: Ontologies and Integrated Data Resources at the Click of the Mouse.L. Whetzel Patricia, H. Shah Nigam, F. Noy Natalya, Dai Benjamin, Dorf Michael, Griffith Nicholas, Jonquet Clement, Youn Cherie, Callendar Chris, Coulet Adrien, Barry Smith, Chris Chute & Mark Musen - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology, Buffalo, NY. pp. 292-293.
    BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  2. Practical Knowledge: Outlines of a Theory of Traditions and Skills.J. C. Nyíri & Barry Smith (eds.) - 1988 - Croom Helm.
    A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.
    Download  
     
    Export citation  
     
    Bookmark   4 citations  
  3. Vagueness and Degrees of Truth, by Nicholas J. J. Smith[REVIEW]Robert Williams - 2011 - Mind 120 (480):1297-1305.
    Download  
     
    Export citation  
     
    Bookmark  
  4. Truth and the Visual Field.Barry Smith - 1999 - In Jean Petitot, F. J. Varela, Bernard Pachoud & J.-M. Roy (eds.), Naturalizing Phenomenology: Issues in Contemporary Phenomenology and Cognitive Science. Stanford: Stanford University Press. pp. 317-329.
    The paper uses the tools of mereotopology (the theory of parts, wholes and boundaries) to work out the implications of certain analogies between the 'ecological psychology' of J. J Gibson and the phenomenology of Edmund Husserl. It presents an ontological theory of spatial boundaries and of spatially extended entities. By reference to examples from the geographical sphere it is shown that both boundaries and extended entities fall into two broad categories: those which exist independently of our cognitive acts (for example, (...)
    Download  
     
    Export citation  
     
    Bookmark   15 citations  
  5.  87
    La vérité et le champ visuel.Barry Smith - 2002 - In Jean-Michel Roy, Jean Francisco J. Varela & Bernard Pachoud (eds.), Naturaliser la phénoménologie: Husserlianisme et science cognitive. Paris: CNRS Editions. pp. 411-426.
    La présente étude utilise les outils du domaine de la méréotopologie (la théorie des parts, ensembles et frontières) pour élaborer les implications de certaines analogies entre la 'psychologie écologique' de J.J.Gibson et la phénoménologie de Edmund Husserl. On présentera une théorie ontologique de frontières spatiales et des entités possédant une extension spatiale. S'en rapportant aux exemples de la sphère de géographie, on démontre qu'aussi bien les frontières que les entités à extension spatiale appartiennent à deux vastes catégories: des objets qui (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark  
  6. Toward a Realistic Science of Environments.Barry Smith - 2009 - Ecological Psychology 21 (2):121-130.
    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 (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  7. Values in Contexts: An Ontological Theory.Barry Smith - 2015 - In G. John M. Abbarno (ed.), Inherent and Instrumental Values: Excursions in Value Inquiry. University Press of America. pp. 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 (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  8. Kognitionsforskningens topologiske grundlag.Barry Smith - 2003 - Semikolon 3 (7):91-105.
    The paper introduces the concepts at the heart of point-set-topology and of mereotopology (topology founded in the non-atomistic theory of parts and wholes) in an informal and intuitive fashion. It will then seek to demonstrate how mereotopological ideas can be of particular utility in cognitive science applications. The prehistory of such applications (in the work of Husserl, the Gestaltists, of Kurt Lewin and of J. J. Gibson) will be sketched, together with an indication of the field of possibilities in linguistics, (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark  
  9. Husserlian Ecology.Barry Smith - 2001 - Human Ontology (Kyoto) 7:9-24.
    If mind is a creature of adaptation, then our standard theories of intentionality and of mental representation are in need of considerable revision. For such theories, deriving under Cartesian inspiration from the work of Brentano, Husserl and their followers, are context-free. They conceive the subject of mental experience in isolation from any surrounding physico-biological environment. Husserl sought in his later writings to find room for the surrounding world of human practical experience, and a similar expansion of concerns can be detected (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  10.  64
    Les objects sociaux.Barry Smith - 2002 - Philosophique 26 (2):315–347.
    One reason for the renewed interest in Austrian philosophy, and especially in the work of Brentano and his followers, turns on the fact that analytic philosophers have become once again interested in the traditional problems of metaphysics. It was Brentano, Husserl, and the philosophers and psychologists whom they influenced, who drew attention to the thorny problem of intentionality, the problem of giving an account of the relation between acts and objects or, more generally, between the psychological environments of cognitive subjects (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark  
  11.  75
    An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Masci Anna Maria, N. Arighi Cecilia, D. Diehl Alexander, E. Lieberman Anne, Mungall Chris, H. Scheuermann Richard, Barry Smith & G. Cowell Lindsay - 2009 - BMC Bioinformatics 10 (1):70.
    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 (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  12. A Product Life Cycle Ontology for Additive Manufacturing.Munira Mohd Ali, Rahul Rai, J. Neil Otte & Barry Smith - 2019 - Computers in Industry 105:191-203.
    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. (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  13. Comment: Minimal Conditions for the Simplest Form of Self-Consciousness.Adrian J. T. Smith - 2010 - In Thomas Fuchs, Heribert Sattel & Peter Henningsen (eds.), The embodied self: Dimensions, coherence, disorders. Schattauer.
    Commentary on: Olaf Blanke, Thomas Metzinger, Full-body illusions and minimal phenomenal selfhood, Trends in Cognitive Sciences, Volume 13, Issue 1, January 2009, Pages 7-13, ISSN 1364-6613, DOI: 10.1016/j.tics.2008.10.003.
    Download  
     
    Export citation  
     
    Bookmark   3 citations  
  14. Interoperability of Disparate Engineering Domain Ontologies Using Basic Formal Ontology.Thomas J. Hagedorn, Barry Smith, Sundar Krishnamurty & Ian R. Grosse - 2019 - Journal of Engineering Design 31.
    As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...)
    Download  
     
    Export citation  
     
    Bookmark  
  15.  29
    Enriching the Functionally Graded Materials (FGM) Ontology for Digital Manufacturing.Munira Mohd Ali, Ruoyu Yang, Binbin Zhang, Francesco Furini, Rahul Rai, J. Neil Otte & Barry Smith - 2020 - International Journal of Production Research:1-18.
    Functionally graded materials (FGMs) have been used in many different kinds of applications in recent years and have attracted significant research attention. However, we do not yet have a commonly accepted way of representing the various aspects of FGMs. Lack of standardised vocabulary creates obstacles to the extraction of useful information relating to pertinent aspects of different applications. A standard resource is needed for describing various elements of FGMs, including existing applications, manufacturing techniques, and material characteristics. This motivated the creation (...)
    Download  
     
    Export citation  
     
    Bookmark  
  16.  92
    The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.Ramona Lynn Walls, Laurel Cooper, Justin Lee Elser, Maria Alejandra Gandolfo, Christopher J. Mungall, Barry Smith, Dennis William Stevenson & Pankaj Jaiswal - 2019 - Frontiers in Plant Science 10.
    The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...)
    Download  
     
    Export citation  
     
    Bookmark  
  17. Discussion of “Biomedical Informatics: We Are What We Publish”.Geissbuhler Antoine, W. E. Hammond, A. Hasman, R. Hussein, R. Koppel, C. A. Kulikowski, V. Maojo, F. Martin-Sanchez, P. W. Moorman, Moura La, F. G. De Quiros, M. J. Schuemle, Barry Smith & J. Talmon - 2013 - Methods of Information in Medicine 52 (6):547-562.
    This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.
    Download  
     
    Export citation  
     
    Bookmark  
  18.  94
    An Evolutionary Approach to Realism-Based Adverse Event Representations.Werner Ceusters, Maria Capolupo, G. De Moor, J. Devlies & Barry Smith - 2011 - Methods of Information in Medicine 50 (1):62-73.
    One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  19. CARO: The Common Anatomy Reference Ontology.Melissa Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, José L. V. Mejino Jr, Chris J. Mungall & Barry Smith - 2008 - In Anatomy Ontologies for Bioinformatics: Principles and Practice. Springer. pp. 327-349.
    The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark   2 citations  
  20.  80
    Formal Ontology for Biomedical Knowledge Systems Integration.J. M. Fielding, J. Simon & Barry Smith - 2004 - Proceedings of Euromise:12-17.
    The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level (...)
    Download  
     
    Export citation  
     
    Bookmark  
  21.  52
    Six Questions on the Construction of Ontologies in Biomedicine.Anand Kumar, A. Burgun, W. Ceusters, J. Cimino, J. Davis, P. Elkin, I. Kalet, A. Rector, J. Rice, J. Rogers, Barry Smith & Others - 2005 - Report of the AMIA Working Group on Formal Biomedical Knowledge Representation 1.
    (Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...)
    Download  
     
    Export citation  
     
    Bookmark  
  22. Making AI Meaningful Again.Jobst Landgrebe & Barry Smith - 2019 - Synthese:arXiv:1901.02918v1.
    Artificial intelligence (AI) research enjoyed an initial period of enthusiasm in the 1970s and 80s. But this enthusiasm was tempered by a long interlude of frustration when genuinely useful AI applications failed to be forthcoming. Today, we are experiencing once again a period of enthusiasm, fired above all by the successes of the technology of deep neural networks or deep machine learning. In this paper we draw attention to what we take to be serious problems underlying current views of artificial (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  23. An Ontological Approach to Representing the Product Life Cycle.J. Neil Otte, Dimitris Kiritsi, Munira Mohd Ali, Ruoyu Yang, Binbin Zhang, Ron Rudnicki, Rahul Rai & Barry Smith - 2019 - Applied Ontology 14 (2):1-19.
    The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  24. Formal Ontology, Common Sense, and Cognitive Science.Barry Smith - 1995 - International Journal of Human-Computer Studies 43 (5-6):641–667.
    Common sense is on the one hand a certain set of processes of natural cognition - of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...)
    Download  
     
    Export citation  
     
    Bookmark   11 citations  
  25. Naive Physics.Barry Smith & Roberto Casati - 1994 - Philosophical Psychology 7 (2):227 – 247.
    The project of a 'naive physics' has been the subject of attention in recent years above all in the artificial intelligence field, in connection with work on common-sense reasoning, perceptual representation and robotics. The idea of a theory of the common-sense world is however much older than this, having its roots not least in the work of phenomenologists and Gestalt psychologists such as K hler, Husserl, Schapp and Gibson. This paper seeks to show how contemporary naive physicists can profit from (...)
    Download  
     
    Export citation  
     
    Bookmark   18 citations  
  26. The Structures of the Common-Sense World.Barry Smith - 1995 - Acta Philosophica Fennica 58:290–317.
    While contemporary philosophers have devoted vast amounts of attention to the language we use in describing and finding our way about the world of everyday experience, they have, with few exceptions, refused to see this world itself as a fitting object of theoretical concern. In what follows I shall seek to show how the commonsensical world might be treated ontologically as an object of investigation in its own right. At the same time I shall seek to establish how such a (...)
    Download  
     
    Export citation  
     
    Bookmark   12 citations  
  27. L'ontologia del senso commune.Barry Smith - 2004 - In E. Agazzi (ed.), Valore E Limiti Del Senso Comune. Milan: FrancoAngeli. pp. 261-284.
    Common sense is on the one hand a certain set of processes of natural cognition – of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark  
  28. La physique naïve: un essai d'ontologie.Barry Smith & Roberto Casati - 1993 - Intellectica 17 (2):173--197.
    The project of a naive physics has been the subject of attention in recent years above all in the artificial intelligence field, in connection with work on common-sense reasoning, perceptual representation and robotics. The idea of a theory of the common-sense world is however much older than this, having its roots not least in the work of phenomenologists and Gestalt psychologists such as Kohler, Husserl, Schapp and Gibson. This paper seeks to show how contemporary naive physicists can profit from a (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark   1 citation  
  29. Objects and Their Environments: From Aristotle to Ecological Ontology.Barry Smith - 2001 - In Andrew U. Frank, Jonathan Raper & Jean-Paul Cheylan (eds.), The Life and Motion of Socio-Economic Units. London: Taylor & Francis. pp. 79-97.
    What follows is a contribution to the theory of space and of spatial objects. It takes as its starting point the philosophical subfield of ontology, which can be defined as the science of what is: of the various types and categories of objects and relations in all realms of being. More specifically, it begins with ideas set forth by Aristotle in his Categories and Metaphysics, two works which constitute the first great contributions to ontological science. Because Aristotle’s ontological ideas were (...)
    Download  
     
    Export citation  
     
    Bookmark   8 citations  
  30.  60
    New Desiderata for Biomedical Terminologies.Barry Smith - 2008 - In Katherine Munn & Barry Smith (eds.), Applied Ontology: An Introduction. Ontos. pp. 83-109.
    It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys (...)
    Download  
     
    Export citation  
     
    Bookmark   3 citations  
  31.  55
    The Ecological Approach to Information Processing.Barry Smith - 2003 - In Kristóf Nyíri (ed.), Mobile Learning: Essays on Philosophy, Psychology and Education. Passagen Verlag. pp. 17--24.
    Imagine a 5-stone weakling whose brain has been loaded with all the knowledge of a champion tennis player. He goes to serve in his first match – Wham! – His arm falls off. The 5-stone weakling just doesn’t have the bone structure or muscular development to serve that hard. There are, clearly, different types of knowledge/ability/skill, only some of which are a matter of what can be transferred simply by passing signals down a wire from one brain (or computer) to (...)
    Download  
     
    Export citation  
     
    Bookmark   3 citations  
  32.  66
    Die Struktur der Common-Sense Welt.Barry Smith - 1994 - Logos. Anales Del Seminario de Metafísica [Universidad Complutense de Madrid, España] 1:422-449.
    Die zeitgenössischen Philosophen haben zwar der Sprache, die wir verwenden, um die Welt der alltäglichen Erfahrung zu beschreiben oder um uns in dieser Welt zurechtzufinden, große Aufmerksamkeit geschenkt, sie haben sich jedoch – von einigen Ausnahmen abgesehen – geweigert, diese Welt selbst als passendes Objekt theoretischer Betrachtungen anzusehen. Im folgenden werde ich versuchen zu zeigen, wie es möglich ist, die Common-Sense-Welt als ontologisch eigenständiges Untersuchungsobjekt zu verstehen. Gleichzeitig werde ich mich bemühen, deutlich zu zeigen, wie eine solch eigenständige Behandlung uns (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark   1 citation  
  33. A First-Order Logic Formalization of the Industrial Ontology Foundry Signature Using Basic Formal Ontology.Barry Smith, Farhad Ameri, Hyunmin Cheong, Dimitris Kiritsis, Dusan Sormaz, Chris Will & J. Neil Otte - 2019 - In Proceedings of the Joint Ontology Workshops (JOWO), Graz.
    Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...)
    Download  
     
    Export citation  
     
    Bookmark  
  34. The Ontology for Biomedical Investigations.Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel & Jie Zheng - 2016 - PLoS ONE 11 (4):e0154556.
    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 (...)
    Download  
     
    Export citation  
     
    Bookmark   14 citations  
  35. In Defense of Truth: Skepticism, Morality, and The Matrix.Barry Smith & J. Erion Gerald - 2002 - In William Irwin (ed.), Philosophy and The Matrix. Chicago: Open Court. pp. 16-27.
    The Matrix exposes us to the uncomfortable worries of philosophical skepticism in an especially compelling way. However, with a bit more reflection, we can see why we need not share the skeptic’s doubts about the existence of the world. Such doubts are appropriate only in the very special context of the philosophical seminar. When we return to normal life we see immediately that they are groundless. Furthermore, we see also the drastic mistake that Cypher commits in turning his back upon (...)
    Download  
     
    Export citation  
     
    Bookmark  
  36. Towards an Ontology of Pain.Barry Smith, Werner Ceusters, Louis J. Goldberg & Richard Ohrbach - 2011 - In Proceedings of the Conference on Ontology and Analytical Metaphysics. Keio University Press.
    We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pain that is elevated relative to peripheral trauma, (...)
    Download  
     
    Export citation  
     
    Bookmark   6 citations  
  37. The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...)
    Download  
     
    Export citation  
     
    Bookmark   10 citations  
  38. National Center for Biomedical Ontology: Advancing Biomedicine Through Structured Organization of Scientific Knowledge.Daniel L. Rubin, Suzanna E. Lewis, Chris J. Mungall, Misra Sima, Westerfield Monte, Ashburner Michael, Christopher G. Chute, Ida Sim, Harold Solbrig, M. A. Storey, Barry Smith, John D. Richter, Natasha Noy & Mark A. Musen - 2006 - Omics: A Journal of Integrative Biology 10 (2):185-198.
    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 (...)
    Download  
     
    Export citation  
     
    Bookmark   4 citations  
  39. Finding Our Way Through Phenotypes.Andrew R. Deans, Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot, Sándor Csösz, Hong Cui, Barry Smith & Others - 2015 - PLoS Biol 13 (1):e1002033.
    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 (...)
    Download  
     
    Export citation  
     
    Bookmark  
  40. Ontologies as Integrative Tools for Plant Science.Ramona Walls, Balaji Athreya, Laurel Cooper, Justin Elser, Maria A. Gandolfo, Pankaj Jaiswal, Christopher J. Mungall, Justin Preece, Stefan Rensing, Barry Smith & Dennis W. Stevenson - 2012 - American Journal of Botany 99 (8):1263–1275.
    Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark   4 citations  
  41. Protein Ontology: A Controlled Structured Network of Protein Entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...)
    Download  
     
    Export citation  
     
    Bookmark  
  42. Plato on Knowledge as a Power.Nicholas D. Smith - 2000 - Journal of the History of Philosophy 38 (2):145-168.
    Download  
     
    Export citation  
     
    Bookmark   7 citations  
  43. Ontology and the Future of Dental Research Informatics.Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick - 2010 - Journal of the American Dental Association 141 (10):1173-75.
    How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  44. The Environment Ontology: Contextualising Biological and Biomedical Entities.Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J. Mungall & Suzanna E. Lewis - 2013 - Journal of Biomedical Semantics 4 (43):1-9.
    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, (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  45. Towards a Phenomenology of Repression. A Husserlian Reply to the Freudian Challenge.Nicholas Smith - 2010 - Stockholm University Press.
    This is the first book-length philosophical study of Husserl’s transcendental phenomenology and Freud’s theory of the unconscious. The book investigates the possibility for Husserl’s transcendental phenomenology to clarify Freud’s concept of the unconscious with a focus on the theory of repression as its centre. Repression is the unconscious activity of pushing something away from consciousness, while making sure that it remains active as something foreign within us. How this is possible is the main problem addressed in the work. Unlike previous (...)
    Download  
     
    Export citation  
     
    Bookmark   3 citations  
  46. The Temporality of Sexual Life in Husserl and Freud.Nicholas Smith - 2012 - Phenomenology of Eros.
    In this text I would like to show two things. Firstly, that the so-called “timelessness” of the Freudian unconscious can be elucidated through an interpretation of the concept of Nachträglichkeit, and showing thereby that there is indeed a temporality specific to the workings of the unconscious. Freud’s analysis of early psychic trauma related to sexual phenomena pointed to a serious complication for all believers in the immediate transparency of consciousness. For the “wound” itself was constituted over time, and the possibility (...)
    Download  
     
    Export citation  
     
    Bookmark  
  47. On Creativity and the Philosophy of the Supranational State.Barry Smith & Wolfgang Grassl - 2004 - In Tamás Demeter (ed.), Essays on Wittgenstein and Austrian Philosophy: In Honour of J.C. Nyíri. Rodopi. pp. 25-39.
    Building on the writings of Wittgenstein on rule-following and deviance, Kristóf Nyíri advanced a theory of creativity as consisting in a fusion of conflicting rules or disciplines. Only such fusion can produce something that is both intrinsically new and yet capable of being apprehended by and passed on to a wider community. Creativity, on this view, involves not the breaking of rules, or the deliberate cultivation of deviant social habits, but rather the acceptance of enriched systems of rules, the adherence (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  48. “… (Why Husserl) … (Why Husserl is More Contemporary Than Time Itself) … (Time Itself) …”.Nicholas Smith - 2009 - SITE Magazine (26-27).
    Even though Husserl’s thinking has received a remarkable amount of attention over the last decades, the full extent of many of its central aspects still remains surprisingly unknown. It is in particular the development of genetic phenomenology that is at stake here, as it plunges ever deeper into “originary constitution” ferreting out the structural relations between inner time-consciousness, affectivity and intersubjectivity, while at the same time never giving up static phenomenology and a certain prioritizing of Cartesian subjectivity. In the following (...)
    Download  
     
    Export citation  
     
    Bookmark  
  49.  33
    Foucault sobre ética y subjetividad: ‘cuidado de sí’ y ‘estética de la existencia.Daniel J. Smith - 2017 - Dorsal. Revista de Estudios Foucaultianos 2:301-321.
    Este ensayo considera la estructura del sujeto ético que se encuentra en los últimos trabajos de Foucault sobre ética, y da cuenta de sus dos conceptos éticos fundamentales: “cuidado de sí” y “estética de la existencia”. El “cuidado de sí”, se argumenta, da a Foucault una manera de conceptualizar la ética que no depende de categorías jurídicas, y que no concibe al sujeto ético en el modelo de la sustancia. “El cuidado de sí” conlleva una comprensión del sujeto ético como (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark  
  50.  77
    Protein-Centric Connection of Biomedical Knowledge: Protein Ontology Research and Annotation Tools.Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Barry Smith & Others - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology. Buffalo, NY: NCOR. pp. 285-287.
    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.
    Download  
     
    Export citation  
     
    Bookmark  
1 — 50 / 1000