Ontology

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  1. Drawing Boundaries.Barry Smith - 2019 - In Timothy Tambassi (ed.), The Philosophy of GIS. New York: Springer. pp. 137-158.
    In “On Drawing Lines on a Map” (1995), I suggested that the different ways we have of drawing lines on maps open up a new perspective on ontology, resting on a distinction between two sorts of boundaries: fiat and bona fide. “Fiat” means, roughly: human-demarcation-induced. “Bona fide” means, again roughly: a boundary constituted by some real physical discontinuity. I presented a general typology of boundaries based on this opposition and showed how it generates a corresponding typology of the different sorts (...)
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  2. (June 2019 to 2014) The UNBELIEVABLE Similarities Between the Ideas of Some People (2011-2016) and My Ideas (2002-2008) in Physics (Quantum Mechanics, Cosmology), Cognitive Neuroscience, Philosophy of Mind, and Philosophy.Gabriel Vacariu - manuscript
    COTENT -/- (April 2019) Why so many people (from so many countries/domains/on so many topics) have already plagiarized my ideas? (Gabriel Vacariu) -/- Some preliminary comments Introduction: The EDWs perspective in my article from 2005 and my book from 2008 -/- I. PHYSICS, COGNITIVE NEUROSCIENCE, PHILOSOPHY (‘REBORN DINOSAURS’) • (2016) Sean Carroll (California Institute of Technology, USA) • (2016) Frank Wilczek (Nobel Prize in Physics) • (2017-2019 - NEW March 2019) Carlo Rovelli in three books (2015, 2017) to my ideas (...)
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  3. Structure, Intentionality and the Given.M. Oreste Fiocco - forthcoming - In Christoph Limbeck-Lilienau & Friedrich Stadler (eds.), The Philosophy of Perception and Observation: Proceedings of the 40th International Wittgenstein Symposium. Berlin, Germany: De Gruyter.
    The given is the state of a mind in its primary engagement with the world. A satisfactory epistemology—one, it turns out, that is foundationalist and includes a naïve realist view of perception—requires a certain account of the given. Moreover, knowledge based on the given requires both a particular view of the world itself and a heterodox account of judgment. These admittedly controversial claims are supported by basic ontological considerations. I begin, then, with two contradictory views of the world per se (...)
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  4. 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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  5. (April 2019) Gabriel Vacariu “Why so Many People (From so Many Countries/Domains/on so Many Topics) Have Already Plagiarized My Ideas?”.Gabriel Vacariu - manuscript
    Since 2015, incredible many have published UNBELIEVABLE similar ideas to my ideas published between 2002-2008!!! There were others who published UNBELIEVABLE similar ideas to my ideas even earlier (since 2008, in general), but the number has an incredible jump after 2014. Why? In 2014, I have sent emails to thousands of people (many countries, many domains (Physics, Philosophy, and Cognitive Science)) regarding the UNBELIEVABLE similarities between my ideas (2002-2008) and Markus Gabriel’s ideas (his book from 2013). Is it this a (...)
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  6. Gabriel Vacariu (Second April 2019 to 2014) The UNBELIEVABLE Similarities Between the Ideas of Some People (2011-2016) and My Ideas (2002-2008) in Physics (Quantum Mechanics, Cosmology), Cognitive Neuroscience, Philosophy of Mind, and Philosophy (This Manuscript Would Require a REVOLUTION in International Academy Environment!). [REVIEW]Gabriel Vacariu - manuscript
    COTENT -/- (second April 2019) Why so many people (from so many countries/domains/on so many topics) have already plagiarized my ideas? (Gabriel Vacariu) -/- Some preliminary comments Introduction: The EDWs perspective in my article from 2005 and my book from 2008 -/- I. PHYSICS, COGNITIVE NEUROSCIENCE, PHILOSOPHY (‘REBORN DINOSAURS’ ) • (2016) Did Sean Carroll’s ideas (California Institute of Technology, USA) plagiarize my ideas (2002-2010) (within the EDWs framework)? • (2016) Frank Wilczek’s ideas (Nobel Prize in Physics) (Philosophy of Mind (...)
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  7. Time's Arrow in a Quantum Universe: On the Status of Statistical Mechanical Probabilities.Eddy Keming Chen - forthcoming - In Valia Allori (ed.), Statistical Mechanics and Scientific Explanation: Determinism, Indeterminism and Laws of Nature. World Scientific.
    In a quantum universe with a strong arrow of time, it is standard to postulate that the initial wave function started in a particular macrostate---the special low-entropy macrostate selected by the Past Hypothesis. Moreover, there is an additional postulate about statistical mechanical probabilities according to which the initial wave function is a ''typical'' choice in the macrostate. Together, they support a probabilistic version of the Second Law of Thermodynamics: typical initial wave functions will increase in entropy. Hence, there are two (...)
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  8. Understanding Universals in Abelard's Tractatus de Intellectibus: The Notion of "Nature".Roxane Noël - 2018 - Dissertation, University of Alberta
    This thesis focuses on Abelard’s solution to the problem of understanding universals as presented in the Tractatus de Intellectibus. He examines this issue by asking what is understood when we consider the term ‘man’, a problem I call the ‘homo intelligitur [man is understood]’ problem. This is an important question, since earlier in the Treatise, Abelard states that understandings paying attention [attendens] to things otherwise than they are are empty, and thus, cannot be true. The challenge is therefore to explain (...)
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  9. Philosophy for Girls: Book Proposal.Melissa Shew & Kim Garchar - forthcoming
    This forthcoming edited volume is written by expert women in philosophy for younger women and girls ages 16-20. It features a range of ethical, metaphysical, social and political, and other philosophical chapters divided into four main sections. Each chapter features an opening anecdote involving women and/or girls from historical, literary, artistic, scientific, mythic, and other sources to lead into the main topic of the chapter.
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  10. Sellars' Argument for an Ontology of Absolute Processes.David Landy - 2019 - Journal for the History of Analytical Philosophy 7 (1):1-25.
    Scholars have rejected Wilfrid Sellars’ argument for an ontology of absolute processes on the grounds that it relies on a dubious and dogmatic appeal to the homogeneity of color. Borrowing from Rosenthal’s recent defense, but ultimate rejection of homogeneity, I defend this claim of on Sellarsian/Kantian transcendental grounds, and reconstruct the remainder of his argument. I argue that Sellars has good reason to suppose that homogeneity is a necessary condition of any possible experience, including indirect experience of theoretical-explanatory posits, and (...)
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  11. The Rise of the Technobionts: Toward a New Ontology to Understand Current Planetary Crisis.Gustavo Magallanes Guijón & O. López-Corona - forthcoming - Researchers.One.
    Inhere we expand the concept of Holobiont to incorporate niche construction theory in order to increase our understanding of the current planetary crisis. By this, we propose a new ontology, the Ecobiont, as the basic evolutionary unit of analysis. We make the case of Homo Sapiens organized around modern cities (technobionts) as a different Ecobiont from classical Homo Sapiens (i.e. Hunter- gatherers Homo Sapiens). We consider that Ecobiont ontology helps to make visible the coupling of Homo Sapiens with other biological (...)
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  12. The Nonclassical Mereology of Olfactory Experiences.Błażej Skrzypulec - forthcoming - Synthese:1-20.
    While there is a growing philosophical interest in analysing olfactory experiences, the mereological structure of odours considered in respect of how they are perceptually experienced has not yet been extensively investigated. The paper argues that odours are perceptually experienced as having a mereological structure, but this structure is significantly different from the spatial mereological structure of visually experienced objects. Most importantly, in the case of the olfactory part-structure, the classical weak supplementation principle is not satisfied. This thesis is justified by (...)
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  13. Consciousness and Meaning: Selected Essays.Katalin Balog & Stephanie Beardman (eds.) - 2017 - Oxford University Press.
    One of the most important problems of modern philosophy concerns the place of subjectivity in a purely physical universe. Brian Loar was a major contributor to the discussion of this problem for over four decades. This volume brings together his most important and influential essays in the philosophy of language and of mind.
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  14. 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 (...)
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  15. Schleiermacher Between Kant and Leibniz.Jacqueline Mariña - 2004 - In Christine Helmer & Marjorie Suchocki (eds.), Schleiermacher and Whitehead: Open Systems in Dialogue.
    This paper takes stock of Leibnizian influences on Schleiermacher's thought through an examination and comparison of the views of Leibniz, Kant, and Schleiermacher on predication. I analyze each thinker's foundational ontological and epistemological commitments and their implications for their understanding of predication. More specifically, I explore whether Schleiermacher's adoption of Leibiniz' theory of the complete concept and the theory of prediction it entails conflicts with his adoption of Kant's two-source theory of knowledge. I conclude that it does, and that it (...)
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  16. 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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  17. Fiat Objects.Barry Smith - 1994 - In Nicola Guarino, Laure Vieu & Simone Pribbenow (eds.), Parts and Wholes: Conceptual Part-Whole Relations and Formal Mereology, 11th European Conference on Artificial Intelligence, Amsterdam, 8 August 1994, Amsterdam:. Amsterdam: European Coordinating Committee for Artificial Intelligence. pp. 14-22.
    Human cognitive acts are directed towards entities of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. A categorial scheme for the objects of human cognition should be (1) critical and realistic. Cognitive subjects are liable to error, even to systematic error of the sort that is manifested by believers in the Pantheon of Olympian gods. Thus not all putative object-directed acts should be recognized as having objects of their own. (...)
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  18. Mereological Composition and Plural Quantifier Semantics.Manuel Lechthaler & Ceth Lightfield - 2018 - Philosophia 46 (4):943-958.
    Mereological universalists and nihilists disagree on the conditions for composition. In this paper, we show how this debate is a function of one’s chosen semantics for plural quantifiers. Debating mereologists have failed to appreciate this point because of the complexity of the debate and extraneous theoretical commitments. We eliminate this by framing the debate between universalists and nihilists in a formal model where these two theses about composition are contradictory. The examination of the two theories in the model brings clarity (...)
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  19. Aristotle's Axology.Seyed Mohammad Hosseini - 2010 - Ayeneh Marefat 20 (7):95-121.
    This Paper attempts to Jude the axiology of Aristotle’s Philosophy based on Aristotelian Philosophy. For this Purpose, we will first Prove axiology as a kind of knowledge and then we will study the relation between axiology and two others knowledge domains, that is, ontology and epistemology. We will demonstrate that values like goodness and beauty, are same final cause and formal cause for explanation of values of every thing. At least, in the nature, goodness and beauty are the idea of (...)
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  20. SNOMED CT Standard Ontology Based on the Ontology for General Medical Science.Shaker El-Sappagh, Francesco Franda, Ali Farman & Kyung-Sup Kwak - 2018 - BMC Medical Informatics and Decision Making 76 (18):1-19.
    Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way that will (...)
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  21. Ontology-Based Fusion of Sensor Data and Natural Language.Erik Thomsen & Barry Smith - 2018 - Applied Ontology 13 (4):295-333.
    We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds of (...)
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  22. Biomedical Ontology Alignment: An Approach Based on Representation Learning.Prodromos Kolyvakis, Alexandros Kalousis, Barry Smith & Dimitris Kiritsis - 2018 - Journal of Biomedical Semantics 9 (21).
    While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic (...)
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  23. On Defining Bruxism.W. Ceusters & B. Smith - 2018 - Studies in Health Technology and Informatics 247:551-555.
    In a series of recent publications, orofacial researchers have debated the question of how ‘bruxism’ should be defined for the purposes of accurate diagnosis and reliable clinical research. Following the principles of realism-based ontology, we performed an analysis of the arguments involved. This revealed that the disagreements rested primarily on inconsistent use of terms, so that issues of ontology were thus obfuscated by shortfalls in terminology. In this paper, we demonstrate how bruxism terminology can be improved by paying attention to (...)
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  24. 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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  25. Trouble Up at T’Ontological Mill: An Inconclusive Dialog.Peter Simons - 2017 - Cosmos + Taxis 4 (4):64-66.
    Grenon and Smith (2004) propose a framework for the ontology of things in space and time involving and invoking the distinction between continuants and occurrents, which has become a key element of Basic Formal Ontology (BFO). The terminology of SNAP (from “snapshot:” state of a continuant at a time) and SPAN (how an occurrent develops over an interval or timespan) occurs in that paper’s title. While any commonsense ontology will have a place for both continuants and occurrents, there is much (...)
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  26. Jacques Derrida, Hans-Georg Gadamer, Philippe Lacoue-Labarthe, “Heidegger, Philosophy, and Politics: The Heidelberg Conference”. [REVIEW]Facundo Bey - 2017 - Phenomenological Reviews 3.
    Heidegger, Philosophy, and Politics: The Heidelberg Conference Autor: Jacques Derrida, Hans-Georg Gadamer, and Philippe Lacoue-Labarthe, Edited by Mireille Calle-Gruber, Translated by Jeff Fort, Foreword by Jean-Luc Nancy, Editorial: Fordham University Press, Fecha de Publicación: 2016, Formato: Hardback $85.00, Páginas: 116, Reviewed by: Facundo Bey (Universidad Nacional de General San Martín / CONICET-Universidad de Buenos Aires).
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  27. The Singularities as Ontological Limits of the General Relativity.Nicolae Sfetcu - manuscript
    The singularities from the general relativity resulting by solving Einstein's equations were and still are the subject of many scientific debates: Are there singularities in spacetime, or not? Big Bang was an initial singularity? If singularities exist, what is their ontology? Is the general theory of relativity a theory that has shown its limits in this case? In this essay I argue that there are singularities, and the general theory of relativity, as any other scientific theory at present, is not (...)
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  28. Fundamental Yet Ontologically Dependent.Joaquim Giannotti - manuscript
    The notion of fundamentality is supposed to play an important role in philosophical inquiry and scientific theorising. Yet there is no consensus on how to formulate it in precise terms. According to a promising view, fundamentality is a form of ontological independence. This view has the merit of capturing a natural connection between fundamentality and ontological dependence. However, it has been recently argued that it is possible that there are fundamental and yet ontologically dependent entities; therefore, we should not characterise (...)
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  29. The Universe as a Computer Game, From Virtual to Actual Reality.Alfred Driessen - 2018 - Scientia et Fides 6 (1):31-52.
    From the very beginning of ancient Greek philosophy up to the present day a puzzling correlation is found between rationality and reality. In this study this relation is examined with emphasis on the philosophical tradition of Aristotle and Aquinas. A comparison is made with the virtual reality created by computers and actual reality of our universe. The view expressed in the scientific neopositivism of Jordan and Mach is found to be an adequate approach to avoid contradictions in the interpretation of (...)
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  30. Interdyscyplinarne Perspektywy Rozwoju, Integracji I Zastosowań Ontologii Poznawczych.Joanna Hastings, Gwen A. Frishkoff, Barry Smith, Mark Jensen, Russell A. Poldrack, Jane Lomax, Anita Bandrowski, Fahim Imam, Jessica A. Turner & Maryann E. Martone - 2016 - Avant: Trends in Interdisciplinary Studies 7 (3):101-117.
    We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...)
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  31. Ontology.Barry Smith - 2003 - In Luciano Floridi (ed.), Blackwell Guide to the Philosophy of Computing and Information. Oxford: Blackwell. pp. 155-166.
    Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by philosophers, the (...)
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  32. Die Ontologie des Embryos.Barry Smith & Berit Brogaard - 2008 - In Ludger Jansen & Barry Smith (eds.), Biomedizinische Ontologie: Wissen strukturieren für den Informatik-Einsatz. Zurich: UTB Forum (vdf). pp. 199-228.
    Der Abschluß der Gastrulation, der gleichzeitig auch den Anfang der Neurulation bedeutet, ist die zeitliche Grenze, die Beginn eines menschlichen Individuums markiert. Oft wird behauptet, daß jegliche natürliche Veränderung stetig ist. Wie ist es dann aber möglich, eine zeitliche Grenze auszuzeichnen, an der ein menschliches Lebewesen zu existieren beginnt? Man beachte, was geschieht, wenn wir vom Thema zeitlicher Unstetigkeit zum räumlichen übergehen. Lebewesen haben räumliche Grenzen (wie sie durch ihre Haut geformt wird). Die letzteren sind genuine Diskontinuitäten, auch angesichts der (...)
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  33. Sechzehn Tage: Wann Beginnt Ein Menschliches Leben?Barry Smith & Berit Brogaard - 2006 - In Guido Imaguire & Christine Schneider (eds.), Untersuchungen zur Ontologie. Munich: Philosophia. pp. 3-40.
    Der Abschluß der Gastrulation, der gleichzeitig auch den Anfang der Neurulation bedeutet, ist die zeitliche Grenze, die Beginn eines menschlichen Individuums markiert. Oft wird behauptet, daß jegliche natürliche Veränderung stetig ist. Wie ist es dann aber möglich, eine zeitliche Grenze auszuzeichnen, an der ein menschliches Lebewesen zu existieren beginnt? Man beachte, was geschieht, wenn wir vom Thema zeitlicher Unstetigkeit zum räumlichen übergehen. Lebewesen haben räumliche Grenzen (wie sie durch ihre Haut geformt wird). Die letzteren sind genuine Diskontinuitäten, auch angesichts der (...)
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  34. ImmPort, Toward Repurposing of Open Access Immunological Assay Data for Translational and Clinical Research.Sanchita Bhattacharya, Patrick Dunn, Cristel Thomas, Barry Smith, Henry Schaefer, Jieming Chen, Zicheng Hu, Kelly Zalocusky, Ravi Shankar & Shai Shen-Orr - 2018 - Scientific Data 5:180015.
    Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data (...)
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  35. The Interplay Between Models and Observations.Claudio Masolo, Alessander Botti Benevides & Daniele Porello - 2018 - Applied Ontology 13 (1):41-71.
    We propose a formal framework to examine the relationship between models and observations. To make our analysis precise,models are reduced to first-order theories that represent both terminological knowledge – e.g., the laws that are supposed to regulate the domain under analysis and that allow for explanations, predictions, and simulations – and assertional knowledge – e.g., information about specific entities in the domain of interest. Observations are introduced into the domain of quantification of a distinct first-order theory that describes their nature (...)
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  36. De-Briefing Aime Project : A Participant Perspective.Terence Blake - 2016 - In Bruno Latour (ed.), reset MODERNITY! London, ENGLAND: The MIT Press. pp. 468-474.
    This paper attempts to evaluate the AIME project immanently, from the perspective of a participant, in terms of five criteria: digitality, diplomacy, religiosity, testability, and democracy. A sixth criterion runs through the other five: pluralism. I distinguish between AIME as project, as process, and as party line.
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  37. A Visual Representation of Part-Whole Relationships in BFO-Conformant Ontologies.Jose M. Parente de Oliveira & Barry Smith - 2017 - In Á Rocha, A. M. Correia, H. Adeli, L. P. Reis & S. Costanzo (eds.), Recent Advances in Information Systems and Technologies (Advances in Intelligent Systems and Computing, 569). New York: Springer. pp. 184-194.
    In the visual representation of ontologies, in particular of part-whole relationships, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations, and we propose instead a new representation of part-whole structures for ontologies, and describe the results of experiments designed to show the effectiveness of this new proposal especially as concerns reduction of visual complexity. The proposal is developed to serve visualization of ontologies conformant to the (...)
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  38. Guidelines for Writing Definitions in Ontologies.Selja Seppälä, Alan Ruttenberg & Barry Smith - 2017 - Ciência da Informação 46 (1): 73-88.
    Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integrity of ontologies and reason over data annotated (...)
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  39. Ontologie des Embryos: Wann Beginnt Menschliches Leben.Barry Smith & Berit Brogaard - 2007 - In L. Honnefelder & M. C. Schmidt (eds.), Naturalismus als Paradigma - Wie weit reicht die naturwissenschaftliche Erklärung des Menschen? , 2007,. Berlin: Berlin University Press. pp. 196-204.
    Der Abschluß der Gastrulation, der gleichzeitig auch den Anfang der Neurulation bedeutet, ist die zeitliche Grenze, die Beginn eines menschlichen Individuums markiert. Oft wird behauptet, daß jegliche natürliche Veränderung stetig ist. Wie ist es dann aber möglich, eine zeitliche Grenze auszuzeichnen, an der ein menschliches Lebewesen zu existieren beginnt? Man beachte, was geschieht, wenn wir vom Thema zeitlicher Unstetigkeit zum räumlichen übergehen. Lebewesen haben räumliche Grenzen (wie sie durch ihre Haut geformt wird). Die letzteren sind genuine Diskontinuitäten, auch angesichts der (...)
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  40. The Evaluation of Ontologies: Editorial Review Vs. Democratic Ranking.Barry Smith - 2008 - In Proceedings of InterOntology (Tokyo, Japan, 26-27 February 2008),. Tokyo: Keio University Press. pp. 127-138.
    Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in support of scientific advance. This very success, however, has led to a (...)
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  41. Ontology-Based Integration of Medical Coding Systems and Electronic Patient Records.W. Ceusters, Barry Smith & G. De Moor - 2004 - IFOMIS Reports.
    In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at the (...)
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  42. Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration.James M. Fielding, Jonathan Simon, Werner Ceusters & Barry Smith - 2004 - In Proceedings of the Ninth International Conference on the Principles of Knowledge Representation and Reasoning (KR2004), Whistler, BC, 2-5 June 2004. AMIA. pp. 114–120.
    Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...)
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  43. Ontology and Geographic Objects: An Empirical Study of Cognitive Categorization.David M. Mark, Barry Smith & Barbara Tversky - 1999 - In C. Freksa & David M. Mark (eds.), Spatial Information Theory. Cognitive and Computational Foundations of Geographic Information Science (Lecture Notes in Computer Science 1661). pp. 283-298.
    Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...)
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  44. Ontology, Natural Language, and Information Systems: Implications of Cross-Linguistic Studies of Geographic Terms.David M. Mark, Werner Kuhn, Barry Smith & A. G. Turk - 2003 - In 6th Annual Conference of the Association of Geographic Information Laboratories for Europe (AGILE). pp. 45-50.
    Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological (...)
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  45. Ontology: Towards a New Synthesis.Barry Smith & Chris Welty - 2001 - In Formal Ontology in Information Systems. New York: ACM Press.
    This introduction to the second international conference on Formal Ontology and Information Systems presents a brief history of ontology as a discipline spanning the boundaries of philosophy and information science. We sketch some of the reasons for the growth of ontology in the information science field, and offer a preliminary stocktaking of how the term ‘ontology’ is currently used. We conclude by suggesting some grounds for optimism as concerns the future collaboration between philosophical ontologists and information scientists.
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  46. Malaria Diagnosis and the Plasmodium Life Cycle: The BFO Perspective.Werner Ceusters & Barry Smith - 2010 - In Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting. Tokyo: Keio University Press. pp. 25-34.
    Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed (...)
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  47. ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology.Barry Smith (ed.) - 2009 - Buffalo: NCOR.
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  48. Biomedical Terminologies and Ontologies: Enabling Biomedical Semantic Interoperability and Standards in Europe (White Paper. European Large-Scale Action on Electronic Health).Bernard de Bono, Mathias Brochhausen, Sybo Dijkstra, Dipak Kalra, Stephan Keifer & Barry Smith - 2009
    In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as a (...)
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  49. 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.
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  50. An Evolutionary Approach to the Representation of Adverse Events.Werner Ceusters, Maria Capolupo, Barry Smith & Georges De Moor - 2009 - Studies in Health Technology and Informatics 150:537-541.
    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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