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Applied Ontology: An Introduction

Frankfurt: ontos (2008)

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  1. Phaedrus. Plato - 1956 - Philosophy and Rhetoric 1 (3):182-183.
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  • Philosophia prima sive Ontologia.Christian Wolff & J. Ecole - 1730 - Les Etudes Philosophiques 17 (2):292-292.
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  • Representation is representation of similarities.Shimon Edelman - 1998 - Behavioral and Brain Sciences 21 (4):449-467.
    Intelligent systems are faced with the problem of securing a principled (ideally, veridical) relationship between the world and its internal representation. I propose a unified approach to visual representation, addressing both the needs of superordinate and basic-level categorization and of identification of specific instances of familiar categories. According to the proposed theory, a shape is represented by its similarity to a number of reference shapes, measured in a high-dimensional space of elementary features. This amounts to embedding the stimulus in a (...)
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  • A Theory of Granular Partitions.Thomas Bittner & Barry Smith - 2003 - In Matt Duckham, Michael F. Goodchild & Michael Worboys (eds.), Foundations of Geographic Information Science. London: Taylor & Francis. pp. 117-151.
    We have a variety of different ways of dividing up, classifying, mapping, sorting and listing the objects in reality. The theory of granular partitions presented here seeks to provide a general and unified basis for understanding such phenomena in formal terms that is more realistic than existing alternatives. Our theory has two orthogonal parts: the first is a theory of classification; it provides an account of partitions as cells and subcells; the second is a theory of reference or intentionality; it (...)
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  • True grid.Barry Smith - 2001 - In Daniel R. Montello (ed.), Spatial Information Theory: Foundations of Geographic Information Science. New York: Springer. pp. 14-27.
    The Renaissance architect, moral philosopher, cryptographer, mathematician, Papal adviser, painter, city planner and land surveyor Leon Battista Alberti provided the theoretical foundations of modern perspective geometry. Alberti’s work on perspective exerted a powerful influence on painters of the stature of Albrecht Dürer, Leonardo da Vinci and Piero della Francesca. But his Della pittura of 1435–36 contains also a hitherto unrecognized ontology of pictorial projection. We sketch this ontology, and show how it can be generalized to apply to representative devices in (...)
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  • Against Fantology.Barry Smith - 2005 - In Johann C. Marek & Maria E. Reicher (eds.), Experience and Analysis. Vienna: HPT&ÖBV. pp. 153-170.
    The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...)
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  • A realism-based approach to the evolution of biomedical ontologies.Barry Smith - 2006 - In Proceedings of the Annual AMIA Symposium. Washington, DC: American Medical Informatics Association. pp. 121-125.
    We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...)
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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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  • Questions: An essay in Daubertian phenomenology.Karl Schuhmann & Barry Smith - 1987 - Philosophy and Phenomenological Research 47 (3):353-384.
    A number of logicians and philosophers have turned their attention in recent years to the problem of developing a logic of interrogatives. Their work has thrown a great deal of light on the formal properties of questions and question-sentences and has led also to interesting innovations in our understanding of the structures of performatives in general and, for example, in the theory of presuppositions. When, however, we examine the attempts of logicians such as Belnap or Åqvist to specify what, precisely, (...)
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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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  • The ontology of the Gene Ontology.Barry Smith, Jennifer Williams & Steffen Schulze-Kremer - 2003 - In Smith Barry, Williams Jennifer & Schulze-Kremer Steffen (eds.), AMIA 2003 Symposium Proceedings. AMIA. pp. 609-613.
    The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain (...)
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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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  • Investigating subsumption in DL-based terminologies: A case study in SNOMED CT.Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun - 2004 - In Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun (eds.), Proceedings of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004). pp. 12-20.
    Formalisms such as description logics (DL) are sometimes expected to help terminologies ensure compliance with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) complies with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED CT classes with respect to these principles. Our major results are: 31% of (...)
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  • Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain.Barry Smith, Waclaw Kusnierczyk, Daniel Schober, & Werner Ceusters - 2006 - In Barry Smith, Waclaw Kusnierczyk, Schober & Werner Ceusters (eds.), Proceedings of KR-MED, CEUR, vol. 222. pp. 57-65.
    Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...)
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  • Parts of Classes.David K. Lewis - 1990 - Blackwell.
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  • The Role of Foundational Relations in the Alignment of Biomedical Ontologies.Barry Smith & Cornelius Rosse - 2004 - In M. Fieschi, E. Coiera & Y.-C. J. Li (eds.), Medinfo. IOS Press. pp. 444-448.
    The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations (...)
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  • The Logic of Biological Classification and the Foundations of Biomedical Ontology.Barry Smith - 2005 - In Dag Westerståhl (ed.), Logic, Methodology and Philosophy of Science. Proceedings of the 12th International Conference. King's College Publication. pp. 505-520.
    Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into hierarchies (...)
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  • 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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  • 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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  • 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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  • [Letter from Gilbert Ryle].Gilbert Ryle - 1932 - Philosophy 7 (26):250 -.
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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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  • Aristotle's Physics.William Aristotle & Charlton - 1970
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  • Human Knowledge: Its Scope and Limits.Bertrand Russell - 2009 - New York, USA: Simon and Schuster.
    This brilliant and controversial work investigates the relationship between 'individual' and 'scientific' knowledge.
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  • Von der mannigfachen Bedeutung des Seienden nach Aristoteles.FranzHG Brentano - 2014 - In Von der Mannigfachen Bedeutung des Seienden Nach Aristoteles. Boston: De Gruyter. pp. 1-196.
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  • Testimony.Arindam Chakrabarti - 1994 - Philosophy and Phenomenological Research 54 (4):965-972.
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  • Testimony: a philosophical study.C. A. J. Coady - 1992 - New York: Oxford University Press.
    Our trust in the word of others is often dismissed as unworthy, because the illusory ideal of "autonomous knowledge" has prevailed in the debate about the nature of knowledge. Yet we are profoundly dependent on others for a vast amount of what any of us claim to know. Coady explores the nature of testimony in order to show how it might be justified as a source of knowledge, and uses the insights that he has developed to challenge certain widespread assumptions (...)
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  • Aristotle and the Principle of Individuation.W. Charlton - 1972 - Phronesis 17 (3):239-249.
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  • Linguistics in Philosophy.Charles E. Caton - 1969 - Philosophical Review 78 (4):518.
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  • Holes and Other Superficialities.Roberto Casati & Achille C. Varzi - 1994 - MIT Press.
    Holes are a good example of the sort of entity that down-to-earth philosophers would be inclined to expel from their ontological inventory. In this work we argue instead in favor of their existence and explore the consequences of this liberality—odd as they might appear. We examine the ontology of holes, their geometry, their part-whole relations, their identity and their causal role, the ways we perceive them. We distinguish three basic kinds of holes: blind hollows, perforating tunnels, and internal cavities, treating (...)
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  • The logical syntax of language.Rudolf Carnap - 1937 - London,: K. Paul, Trench, Trubner & co.. Edited by Amethe Smeaton.
    Available for the first time in 20 years, here is the Rudolf Carnap's famous principle of tolerance by which everyone is free to mix and match the rules of ...
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  • The Logical Syntax of Language.Rudolph Carnap - 1936 - Philosophical Review 46 (5):549-553.
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  • Back to class: A note on the ontology of species.Arthur L. Caplan - 1981 - Philosophy of Science 48 (1):130-140.
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  • Abstract particulars.Keith Campbell - 1990 - Cambridge, Mass., USA: Blackwell.
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  • Einführung in die angewandte Logik.Theodor Bucher - 2019 - Walter de Gruyter GmbH & Co KG.
    To celebrate the 270th anniversary of the De Gruyter publishing house, the company is providing permanent open access to 270 selected treasures from the De Gruyter Book Archive. Titles will be made available to anyone, anywhere at any time that might be interested. The DGBA project seeks to digitize the entire backlist of titles published since 1749 to ensure that future generations have digital access to the high-quality primary sources that De Gruyter has published over the centuries.
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  • Ways and Means.Annetie C. Baier - 1972 - Canadian Journal of Philosophy 1 (3):275 - 293.
    In this paper I shall give reasons for rejecting one type of analysis of the basic constituents of action, and reasons for preferring an alternative approach. I shall discuss the concept of basic action recently presented by Alvin Goldman, who gives an interesting version of the sort of analysis I wish to reject. Goldman agrees with Danto that bodily movements are basic actions, and his definition of ‘basic’ resembles Danto's fairly closely. What is new is a useful concept of level-generation (...)
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  • A Theory of Human Action.Alvin Ira Goldman - 1970 - Englewood Cliffs, NJ, USA: Princeton University Press.
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  • Universals and scientific realism.David Malet Armstrong - 1978 - New York: Cambridge University Press.
    v. 1. Nominalism and realism.--v. 2. A theory of universals.
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  • A World of States of Affairs.D. Armstrong - 1993 - Philosophical Perspectives 7:429-440.
    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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  • Studies on Gottlob Frege and Traditional Philosophy.J. E. Llewelyn - 1969 - Philosophical Quarterly 19 (77):361-362.
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  • Studies on Gottlob Frege and traditional philosophy.Ignacio Angelelli (ed.) - 1967 - Dordrecht,: D. Reidel.
    I wish to express, first of all, my profound gratitude to Professor J. M. Bochenski, without whose assistance the present work would have not been possible. To be concise, I would like to state that his contribution to this book may be viewed at three levels: (1) that of the general spirit, (2) that of the specific ideas, theses or approaches which are expressed in its pages, (3) that of this work qua doctoral dissertation. The general spirit which has guided (...)
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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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  • Kategorien des Zeitlichen: eine Untersuchung der Formen des endlichen Verstandes.Sebastian Rödl - 2005 - Frankfurt am Main: Suhrkamp.
    Die analytische Philosophie hat selbst da, wo sie explizit an Kant anschließt, erhebliche Schwierigkeiten mit dessen Idee eines synthetischen Wissens a priori. Damit verliert sie eine ganze Dimension der philosophischen Tradition. Das vorliegende Buch gewinnt diese Idee zurück, indem es gerade den Anschauungsbezug und damit den Zeitbezug des menschlichen Denkens zum Gegenstand einer logischen Untersuchung macht. Nur wenn man die Zeit als inneres und formbildendes Merkmal des menschlichen Aussagens erkennt, versteht man den Begriff empirischer Wahrheit und sinnlich vermittelter Erkenntnis. In (...)
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  • The foundations of arithmetic: a logico-mathematical enquiry into the concept of number.Gottlob Frege - 1959 - Evanston, Ill.: Northwestern University Press. Edited by J. L. Austin.
    § i. After deserting for a time the old Euclidean standards of rigour, mathematics is now returning to them, and even making efforts to go beyond them. ...
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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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  • Phaedrus. Plato & Harvey Yunis (eds.) - 1956 - New York: Cambridge University Press.
    Ostensibly a discussion about love, the debate in the Phaedrus also encompasses the art of rhetoric and how it should be practised. This new edition contains an introductory essay outlining the argument of the dialogue as a whole and Plato's arguments about rhetoric and eros in particular. The Introduction also considers Plato's style and offers an account of the reception of the dialogue from its composition to the twentieth century. A new Greek text of the dialogue is accompanied by a (...)
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  • 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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  • The Mereology of Events.Robert Allen - 2005 - Sorites.
    I demonstrate here that it is possible for an event to be identical with one of its proper parts, refuting the key premise in Lawrence Lombard's argument for the essentiality of an event's time. I also propose and defend an alternative to his criterion of event identity.
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  • Tropes and Other Things.Cynthia Macdonald - 1998 - In Stephen Laurence & Cynthia Macdonald (eds.), Contemporary Readings in the Foundations of Metaphysics. Malden, Mass.: Wiley-Blackwell.
    Our day-to-day experience of the world regularly brings us into contact with middlesized objects such as apples, dogs, and other human beings. These objects possess observable properties, properties that are available or accessible to the unaided senses, such as redness and roundness, as well as properties that are not so available, such as chemical ones. Both of these kinds of properties serve as valuable sources of information about our familiar middle-sized objects at least to the extent that they enable us (...)
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  • Concepts: Core Readings.Eric Margolis & Stephen Laurence (eds.) - 1999 - MIT Press.
    Concepts: Core Readings traces the develoment of one of the most active areas of investigation in cognitive science. This comprehensive volume brings together the essential background readings on concepts from philosophy, psychology, and linguistics, while providing a broad sampling of contemporary research. The first part of the book centers around the fall of the Classical Theory of Concepts in the face of attacks by W.V.O. Quine, Ludwig Wittgenstein, Eleanor Rosch, and others, emphasizing the emergence and development of the Prototype Theory (...)
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