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Applied Ontology: An Introduction

Frankfurt: ontos (2008)

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  1. Ecological Psychology.Roger Garlock Barker - 1968 - Stanford University Press.
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  • (2 other versions)Philosophy and the Scientific Image Of Man.Wilfrid Sellars - 1963 - In Science, Perception and Reality. London: Routledge & Kegan Paul.
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  • Artificial Intelligence: A Modern Approach.Stuart Jonathan Russell & Peter Norvig (eds.) - 1995 - Prentice-Hall.
    Artificial Intelligence: A Modern Approach, 3e offers the most comprehensive, up-to-date introduction to the theory and practice of artificial intelligence. Number one in its field, this textbook is ideal for one or two-semester, undergraduate or graduate-level courses in Artificial Intelligence. Dr. Peter Norvig, contributing Artificial Intelligence author and Professor Sebastian Thrun, a Pearson author are offering a free online course at Stanford University on artificial intelligence. According to an article in The New York Times, the course on artificial intelligence is (...)
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  • (2 other versions)Aristoteles’ Kategorie des Relativen zwischen Dialektik und Ontologie.Ludger Jansen - 2006 - History of Philosophy & Logical Analysis 9 (1):79-104.
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  • Linguistics in Philosophy.Zeno Vendler - 1967 - Ithaca, N.Y.,: Cornell University Press.
    This book is a major attempt to reconcile the empirical basis of linguistic science with the a priori nature of philosophical reasoning. Its purpose is to show how the methods and findings of linguistic science, especially of transformational grammar, can be used to cast light upon central problems of analytic philosophy. After dealing with recent objections to the use of linguistic techniques in philosophy, the author shows, with great force and clarity, how these techniques can be applied to such problems (...)
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  • (1 other version)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:. 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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  • The structure of knowing : Existential trust as an epistemological category.Hildur Kalman - 1999 - Acta Universitatis Umensis 145.
    This thesis investigates the structure of knowing, and it argues that existential trust is an epistemological category. The aim of the dissertation is to develop a view according to which all human activity is seen as an activity of a lived body, and in which the understanding of the structure of such activity is regarded as central for the solution even of epistemological problems. This view is not rooted in any one philosophical tradition, but circles around activity of the lived (...)
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  • (6 other versions)Ontology.Barry Smith - 2003 - In Luciano Floridi (ed.), The Blackwell guide to the philosophy of computing and information. 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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  • Referent tracking and its applications.Werner Ceusters & Barry Smith - 2007 - In Werner Ceusters & Barry Smith (eds.), Proceedings of the Workshop WWW2007 Workshop i3: Identity, Identifiers, Identification (Workshop on Entity-Centric Approaches to Information and Knowledge Management on the Web), Banff, Canada. CEUR.
    Referent tracking (RT) is a new paradigm, based on unique identification, for representing and keeping track of particulars. It was first introduced to support the entry and retrieval of data in electronic health records (EHRs). Its purpose is to avoid the ambiguity that arises when statements in an EHR refer to disorders or other entities on the side of the patient exclusively by means of compound descriptions utilizing general terms such as ‘pimple on nose’ or ‘small left breast tumor’. In (...)
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  • On the application of formal principles to life science data: A case study in the Gene Ontology.Jacob Köhler, Anand Kumar & Barry Smith - 2004 - In Köhler Jacob, Kumar Anand & Smith Barry (eds.), Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics 2994). Springer. pp. 79-94.
    Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based (...)
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  • Functional Anatomy: A Taxonomic Proposal.Ingvar Johansson, Barry Smith, Katherine Dormandy [nee Munn], Kathleen Elsner, Nikoloz Tsikolia & DIrk Siebert - 2005 - Acta Biotheoretica 53 (3):153-166.
    It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.
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  • Was die philosophische Ontologie zur biomedizinischen Informatik beitragen kann.Barry Smith, Dirk Siebert & Werner Ceusters - 2004 - Information: Wissenschaft Und Praxis 55 (3):143-146.
    Die biomedizinische Forschung hat ein Kommunikationsproblem. Um die Ergebnisse ihrer Arbeit darzustellen, greifen einzelne Forschergruppen auf unterschiedliche und oft inkompatible Terminologien zurück. Für den Fortschritt der modernen Biomedizin ist die Integration dieser Ergebnisse jedoch unabdingbar.
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  • Oncology ontology in the NCI Thesaurus.Anand Kumar & Barry Smith - 2005 - Artificial Intelligence in Medicine:213-220.
    The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...)
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  • Ontology as the core discipline of biomedical informatics: Legacies of the past and recommendations for the future direction of research.Barry Smith & Werner Ceusters - 2007 - In Gordana Dodig Crnkovic & Susan Stuart (eds.), Computation, Information, Cognition: The Nexus and the Liminal.f. Cambridge Scholars Press. pp. 104-122.
    The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...)
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  • Wüsteria.Barry Smith, Werner Ceusters & Rita Temmerman - 2005 - Studies in Health Technology and Informatics 116:647-652.
    The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas – which see terminology work as being focused on the classification of concepts in people’s minds – and we argue that (...)
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  • (1 other version)On the Plurality of Worlds.William G. Lycan - 1988 - Journal of Philosophy 85 (1):42-47.
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  • (1 other version)The Concept of Mind.Gilbert Ryle - 1949 - Revue Philosophique de la France Et de l'Etranger 141:125-126.
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  • On the Plurality of Worlds.David Lewis - 1986 - Revue Philosophique de la France Et de l'Etranger 178 (3):388-390.
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  • (2 other versions)The Open Society and its Enemies.Karl R. Popper - 1952 - Revue Philosophique de la France Et de l'Etranger 142:629-634.
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  • (2 other versions)The Open Society and Its Enemies.K. R. Popper - 1946 - Philosophy 21 (80):271-276.
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  • (2 other versions)Aristoteles’ Kategorie des Relativen zwischen Dialektik und Ontologie.Ludger Jansen - 2006 - History of Philosophy & Logical Analysis 9.
    Like the doctrine of the categories in general, Aristotle’s category of the relative fulfils disparate functions: On the one hand, the category of the pros ti fulfils a dialectic or logical function that aims at the avoidance of fallacies. On the other hand, the category respects the peculiar mode of being of the relative. Taking these two different functions into consideration helps with the interpretation of Aristotle’s two definitions of the relative and his treatment of the properties of the relative (...)
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  • Universals and Scientific Realism.[author unknown] - 1980 - British Journal for the Philosophy of Science 31 (1):69-79.
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  • Parts of Classes.David K. Lewis - 1991 - Mind 100 (3):394-397.
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  • (5 other versions)The View from Nowhere.Thomas Nagel - 1986 - Ethics 98 (1):137-157.
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  • On the Metaphysical Distinction Between Processes and Events.Kathleen Gill - 1993 - Canadian Journal of Philosophy 23 (3):365-384.
    In theMetaphysics, Aristotle pointed out that some activities are engaged in for their own sake, while others are directed at some end. The test for distinguishing between them is to ask, ‘At any time during a period in which someone is Xing, is it also true that they have Xed?’ If both are true, the activity is being done for its own sake. If not, it is being done for the sake of some end other than itself. For example, if (...)
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  • (1 other version)Von Der Mannigfachen Bedeutung Des Seienden Nach Aristoteles.Franz Brentano - 1862 - Boston: Herder.
    diefes thut Ariftoteles. indem er die verfchiedenen Bedeutungen. die nach feiner Beobachtung der Name des Seienden umfaßt. unterfcheidend. die eigentlichen von den uneigentlichen fondert und die let-,tern von der metaphyfifchen ...
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  • Parts: A Study in Ontology.Peter M. Simons - 1987 - Oxford, England: Clarendon Press.
    The relationship of part to whole is one of the most fundamental there is; this is the first and only full-length study of this concept. This book shows that mereology, the formal theory of part and whole, is essential to ontology. Peter Simons surveys and criticizes previous theories, especially the standard extensional view, and proposes a more adequate account which encompasses both temporal and modal considerations in detail. 'Parts could easily be the standard book on mereology for the next twenty (...)
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  • Ideas: General Introduction to Pure Phenomenology.Edmund Husserl - 1931 - New York: Routledge. Edited by William Ralph Boyce Gibson.
    First published in 2002. Routledge is an imprint of Taylor & Francis, an informa company.
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  • Metaphysics and the Origin of Species.Michael T. Ghiselin - 1997 - State University of New York Press.
    _This sweeping discussion of the philosophy of evolutionary biology is based on the revolutionary idea that species are not kinds of organisms but wholes composed of organisms._.
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  • The Four-Category Ontology: A Metaphysical Foundation for Natural Science.Edward Jonathan Lowe - 2005 - Oxford, GB: Clarendon Press.
    E. J. Lowe, a prominent figure in contemporary metaphysics, sets out and defends his theory of what there is. His four-category ontology is a metaphysical system which recognizes four fundamental categories of beings: substantial and non-substantial particulars and substantial and non-substantial universals. Lowe argues that this system has an explanatory power which is unrivalled by more parsimonious theories and that this counts decisively in its favour. He shows that it provides a powerful explanatory framework for a unified account of causation, (...)
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  • Biological Individuality: The Identity and Persistence of Living Entities.Jack Wilson - 1999 - New York: Cambridge University Press.
    What makes a biological entity an individual? Jack Wilson shows that past philosophers have failed to explicate the conditions an entity must satisfy to be a living individual. He explores the reason for this failure and explains why we should limit ourselves to examples involving real organisms rather than thought experiments. This book explores and resolves paradoxes that arise when one applies past notions of individuality to biological examples beyond the conventional range and presents an analysis of identity and persistence. (...)
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  • A World of States of Affairs.D. M. Armstrong - 1996 - New York: Cambridge University Press.
    In this important study D. M. Armstrong offers a comprehensive system of analytical metaphysics that synthesises but also develops his thinking over the last twenty years. Armstrong's analysis, which acknowledges the 'logical atomism' of Russell and Wittgenstein, makes facts the fundamental constituents of the world, examining properties, relations, numbers, classes, possibility and necessity, dispositions, causes and laws. All these, it is argued, find their place and can be understood inside a scheme of states of affairs. This is a comprehensive and (...)
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  • (1 other version)The Philosophy of as If.H. Vaihinger - 2000 - Routledge.
    First published in 2000. Routledge is an imprint of Taylor & Francis, an informa company.
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  • On the Plurality of Worlds.David K. Lewis - 1986 - Malden, Mass.: Wiley-Blackwell.
    This book is a defense of modal realism; the thesis that our world is but one of a plurality of worlds, and that the individuals that inhabit our world are only a few out of all the inhabitants of all the worlds. Lewis argues that the philosophical utility of modal realism is a good reason for believing that it is true.
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  • Human Knowledge: Its Scope and Limits.Bertrand Russell - 1948 - London and New York: Routledge.
    How do we know what we "know"? How did we –as individuals and as a society – come to accept certain knowledge as fact? In _Human Knowledge,_ Bertrand Russell questions the reliability of our assumptions on knowledge. This brilliant and controversial work investigates the relationship between ‘individual’ and ‘scientific’ knowledge. First published in 1948, this provocative work contributed significantly to an explosive intellectual discourse that continues to this day.
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  • (1 other version)The Structure of Science.Ernest Nagel - 1961 - Les Etudes Philosophiques 17 (2):275-275.
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  • Ideen zu einer reinen Phänomenologie und Phänomenologischen Philosophie, Erstes Buch, Allgemeine Einführung in die Reine Phänomenologie.L. O. Kattsoff - 1951 - Philosophy and Phenomenological Research 12 (1):139-139.
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  • Word Meaning and Montague Grammar.David R. Dowty - 1982 - Philosophical Review 91 (2):290-295.
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  • (1 other version)Principles of Systematic Zoology.Ernst Mayr - 1969 - McGraw-Hill.
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  • A hierarchy of species concepts: the denouement in the saga of the species problem.R. L. Mayden - 1997 - In M. F. Claridge, H. A. Dawah & M. R. Wilson (eds.), Species: The units of diversity,. Chapman & Hall. pp. 381–423.
    At least 22 concepts of species are in use today and many of these are notably incompatible in their accounts of biological diversity. Much of the traditional turmoil embodied in the species problem ultimately derives from the packaging of inappropriate criteria for species into a single concept. This results from a traditional conflation of function of concepts with their applications, definitions with concepts, taxonomic categories with groups, and the ontological status of real species with teleological approaches to recover them. Analogous (...)
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  • The Order of Things.Michel Foucault - 1970 - Tavistock.
    Like the latter, it unites into one and the same function the possibility of giving things a sign, of representing one thing by another, and the possibility of causing a sign to shift in relation to what it designates. The four functions that define the ...
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  • An Inquiry Into Meaning and Truth.Bertrand Russell - 1940 - New York: Routledge.
    Bertrand Russell is concerned in this book with the foundations of knowledge. He approaches his subject through a discussion of language, the relationships of truth to experience and an investigation into how knowledge of the structure of language helps our understanding of the structure of the world. This edition includes a new introduction by Thomas Baldwin, Clare College, Cambridge.
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  • The representation of life.Michael Thompson - 1995 - In Rosalind Hursthouse, Gavin Lawrence & Warren Quinn (eds.), Virtues and Reasons: Philippa Foot and Moral Theory: Essays in Honour of Philippa Foot. Oxford: Clarendon Press. pp. 247--296.
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  • On negative and disjunctive properties.Uwe Meixner - 1991 - In Kevin Mulligan (ed.), Language, Truth and Ontology. Dordrecht, Netherland: Kluwer Academic Publishers. pp. 28--36.
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  • (2 other versions)Aristoteles’ Kategorie des Relativen zwischen Dialektik und Ontologie.Ludger Jansen - 2006 - Philosophie­Geschichte Und Logische Analyse 9.
    Like the doctrine of the categories in general, Aristotle’s category of the relative fulfils disparate functions: On the one hand, the category of the pros ti fulfils a dialectic or logical function that aims at the avoidance of fallacies. On the other hand, the category respects the peculiar mode of being of the relative. Taking these two different functions into consideration helps with the interpretation of Aristotle’s two definitions of the relative and his treatment of the properties of the relative (...)
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  • Introduction.Barry Smith & David Woodruff Smith - 1995 - In Barry Smith & David Woodruff Smith (eds.), The Cambridge companion to Husserl. New York: Cambridge University Press.
    Husserl’s philosophy, by the usual account, evolved through three stages: 1. development of an anti-psychologistic, objective foundation of logic and mathematics, rooted in Brentanian descriptive psychology; 2. development of a new discipline of "phenomenology" founded on a metaphysical position dubbed "transcendental idealism"; transformation of phenomenology from a form of methodological solipsism into a phenomenology of intersubjectivity and ultimately (in his Crisis of 1936) into an ontology of the life-world, embracing the social worlds of culture and history. We show that this (...)
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  • Tracking Referents in Electronic Health Records.Werner Ceusters & Barry Smith - 2005 - Studies in Health Technology and Informatics 116:71–76.
    Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in (...)
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  • The Ontology-Epistemology Divide: A Case Study in Medical Terminology.OIivier Bodenreider, Barry Smith & Anita Burgun - 2004 - In Achille C. Varzi & Laure Vieu (eds.), ”, Formal Ontology in Information Systems. Proceedings of the Third International Conference. IOS Press.
    Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (i.e., (...)
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  • Referent Tracking: The Problem of Negative Findings.Werner Ceusters, Peter Elkin & Barry Smith - 2006 - Studies in Health Technology and Informatics 124:741-46.
    The paradigm of referent tracking is based on a realist presupposition which rejects so-called negative entities (congenital absent nipple, and the like) as spurious. How, then, can a referent tracking-based Electronic Health Record deal with what are standardly called ‘negative findings’? To answer this question we carried out an analysis of some 748 sentences drawn from patient charts and containing some form of negation. Our analysis shows that to deal with these sentences we need to introduce a new ontological relationship (...)
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  • Strategies for Referent Tracking in Electronic Health Records.Werner Ceusters & Barry Smith - 2006 - Journal of Biomedical Informatics 39 (3):362-378.
    The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems (...)
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