Results for 'Adrian J. T. Smith'

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  1. 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.
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  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.
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  3. La verità trionfa: Da T. G. Masaryk a Jan Patočka.Barry Smith - 1991 - Discipline Filosofiche 2:207–227.
    Thomas Garrigue Masaryk, later founder and President of the Republic of Czechoslovakia, studied philosophy in the University of Vienna from 1872 to 1876, where he came under the powerful influence of Franz Brentano. We survey the role of Brentano’s philosophy, and especially of his ethics, in Masaryk’s life and work.
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  4. Philosophie, Politik und Wissenschaftliche Weltauffassung: Zur Frage der Philosophie in Österreich und Deutschland.Barry Smith - 2000 - Grazer Philosophische Studien 58 (1):1-22.
    Die Entwicklung der Philosophie in Österreich unterscheidet sich in markanter Weise von der Hauptlinie der philosophischen Entwicklung in Deutschland. Dabei fällt bei der österreichischen Philosophie vor allem die konsequente Orientierung an den Wissenschaften auf. In der philosophiegeschichtlichen Forschung sind für diese Besonderheit der österreichischen Philosophie z. B. von Otto Neurath, Rudolf Haller, Friedrich Stadier und J.C. Nyiri verschiedene Erklärungen vorgeschlagen worden. In diesen spielen in jeweils unterschiedlicher Weise Faktoren der spezifisch österreichischen Entwicklungen in historischer, institutioneller, politischer und religiöser Hinsicht eine (...)
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  5.  54
    Von T. G. Masaryk bis Jan Patočka: Eine philosophische Skizze.Barry Smith - 1993 - In J. Zumr & T. Binder (eds.), T. G. Masaryk und die Brentano-Schule. Prague: Czech Academy of Sciences. pp. 94-110.
    Thomas Garrigue Masaryk, later founder and President of the Republic of Czechoslovakia, studied philosophy in the University of Vienna from 1872 to 1876, where he came under the powerful influence of Franz Brentano. We survey the role of Brentano’s philosophy, and especially of his ethics, in Masaryk’s life and work.
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  6. Wanting What We Don't Want to Want: Representing Addiction in Interoperable Bio-Ontologies.Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan & Barry Smith - 2012 - In Ronald Cornet & Robert Stevens (eds.), Proceeedings of the Third International Conference on Biomedical Ontology. CEUR. pp. 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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  7.  59
    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 (...)
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  8.  85
    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 (...)
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  9. 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. (...)
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  10.  54
    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 (...)
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  11. A Strategy for Improving and Integrating Biomedical Ontologies.Cornelius Rosse, Anand Kumar, Jose L. V. Mejino, Daniel L. Cook, Landon T. Detwiler & Barry Smith - 2005 - In Proceedings of the Annual Symposium of the American Medical Informatics Association. AMIA. pp. 639-643.
    The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...)
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  12. Apology Of Socratic Studies.T. Brickhouse & N. Smith - 2003 - Polis 20 (1-2):108-127.
    In this paper, we defend Socratic studies as a research programme against several recent attacks, including at least one recently published in Polis . Critics have argued that the study of Socrates, based upon evidence mostly or entirely derived from some set of Plato's dialogues, is founded upon faulty and indefensible historical or hermeneutical technique. We begin by identifying what we believe are the foundational principles of Socratic studies, as the field has been pursued in recent years, and we then (...)
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  13.  57
    Rosen's ‘a Creature of Modern Scholarship’ -- A Reply.T. Brickhouse & N. Smith - 1998 - Polis 15 (1-2):13-22.
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  14. 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 (...)
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  15.  48
    Examining Tensions in the Past and Present Uses of Concepts (Preprint).Eden T. Smith - forthcoming - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences.
    Examining tensions between the past and present uses of scientific concepts can help clarify their contributions as tools in experimental practices. This point can be illustrated by considering the concepts of mental imagery and hallucinations: despite debates over their respective referential reliabilities remaining unresolved within their interdependent histories, both are used as independently stable concepts in neuroimaging experiments. Building on an account of how these concepts function as tools structured for pursuit of diverging goals in experiments, this paper explores this (...)
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  16. 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 (...)
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  17. 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 (...)
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  18. 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 (...)
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  19. 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 (...)
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  20. The Structured Uses of Concepts as Tools: Comparing fMRI Experiments That Investigate Either Mental Imagery or Hallucinations.Eden T. Smith - 2018 - Dissertation, University of Melbourne
    Sensations can occur in the absence of perception and yet be experienced ‘as if’ seen, heard, tasted, or otherwise perceived. Two concepts used to investigate types of these sensory-like mental phenomena (SLMP) are mental imagery and hallucinations. Mental imagery is used as a concept for investigating those SLMP that merely resemble perception in some way. Meanwhile, the concept of hallucinations is used to investigate those SLMP that are, in some sense, compellingly like perception. This may be a difference of degree. (...)
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  21. 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 (...)
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  22. 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, (...)
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  23. The Planteome Database: An Integrated Resource for Reference Ontologies, Plant Genomics and Phenomics.Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin L. Elser, Chris Mungall, Brandon T. Sinn, Dario Cavaliere, Seth Carbon, Nathan A. Dunn, Barry Smith, Botong Qu, Justin Preece, Eugene Zhang, Sinisa Todorovic, Georgios Gkoutos, John H. Doonan, Dennis W. Stevenson, Elizabeth Arnaud & Pankaj Jaiswal - 2018 - Nucleic Acids Research 46 (D1):D1168–D1180.
    The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...)
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  24. 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 (...)
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  25. 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 (...)
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  26. 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, (...)
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  27. 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 (...)
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  28.  46
    Examining the Structured Uses of Concepts as Tools: Converging Insights.Eden T. Smith - 2019 - Filozofia Nauki 4 (28):7-22.
    Examining the historical development of scientific concepts is important for understanding the structured routines within which these concepts are currently used as goal-directed tools in experiments. To illustrate this claim, I will outline how the concepts of mental imagery and hallucinations each draw on an older interdependent set of associations that, although nominally-discarded, continues to structure their current independent uses for pursuing discrete experimental goals. In doing so, I will highlight how three strands of literature offer mutually instructive insights for (...)
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  29. 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, (...)
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  30. 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.
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  31. A Domain Ontology for the Non-Coding RNA Field.Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang & Yu Lin - 2015 - In IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015). pp. 621-624.
    Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.
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  32. 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 (...)
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  33. Bioinformatics Advances in Saliva Diagnostics.Ji-Ye Ai, Barry Smith & David T. W. Wong - 2012 - International Journal of Oral Science 4 (2):85--87.
    There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva (...)
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  34. 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 (...)
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  35.  94
    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 (...)
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  36. 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 (...)
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  37. 'Von der Armut Am Geiste': A Dialogue by the Young Lukács.Jane M. Smith & John T. Sanders - 2009 - In Katie Terezakis (ed.), Engaging Agnes Heller: A Critical Companion. Lexington Books.
    Translation of "Von der Armut am Geiste; ein Dialog des jungen Lukács," by Ágnes Heller. This translation originally appeared in The Philosophical Forum, Spring-Summer 1972.
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  38. 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 (...)
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  39. 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, (...)
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  40. 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.
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  41. 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, (...)
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  42. 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 (...)
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  43. 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 (...)
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  44.  86
    Interdependent Concepts and Their Independent Uses: Mental Imagery and Hallucinations.Eden T. Smith - 2018 - Perspectives on Science 26 (3):360-399.
    The scientific concepts of mental imagery and hallucinations are each used independently of the other; uses that simultaneously evoke and obscure their historical connections. In this paper, I aim to illustrate the relevance of examining one of these historical connections for studying the current uses of these two concepts in neuroimaging experiments. To this end, I will highlight interdependent associations within the histories of each of the concepts that continue to contribute to their independent uses.That mental imagery and hallucinations are (...)
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  45. 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 (...)
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  46.  40
    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 (...)
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  47.  81
    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.
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  48.  83
    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 (...)
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  49.  73
    The Non-Coding RNA Ontology : A Comprehensive Resource for the Unification of Non-Coding RNA Biology.Huang Jingshan, Eilbeck Karen, Barry Smith, A. Blake Judith, Dou Dejing, Huang Weili, A. Natale Darren, Ruttenberg Alan, Huan Jun & T. Zimmermann Michael - 2016 - Journal of Biomedical Semantics 7 (1).
    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...)
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  50.  72
    OmniSearch: A Semantic Search System Based on the Ontology for MIcroRNA Target Gene Interaction Data.Huang Jingshan, Gutierrez Fernando, J. Strachan Harrison, Dou Dejing, Huang Weili, A. Blake Judith, Barry Smith, Eilbeck Karen, A. Natale Darren & Lin Yu - 2016 - Journal of Biomedical Semantics 7 (1):1.
    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...)
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