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Applied Ontology: An Introduction

Frankfurt: ontos (2008)

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  1. 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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  • (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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  • 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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  • Ontology with Human Subjects Testing: An Empirical Investigation of Geographic Categories.Barry Smith & David M. Mark - 1998 - American Journal of Economics and Sociology 58 (2):245–272.
    Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological theorizing in abstract (...)
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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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  • 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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  • Relations in Biomedical Ontologies.Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kuma, Jane Lomax, Chris Mungall, , Fabian Neuhaus, Alan Rector & Cornelius Rosse - 2005 - Genome Biology 6 (5):R46.
    To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.
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  • The Last Word.Thomas Nagel - 1997 - Oxford: Oxford University Press.
    In this important new book Nagel, one of the most distinguished philosophers writing in English today, presents a sustained defence of reason against the attacks of subjectivism. He offers systematic rebuttals of relativistic claims with respect to language, logic, science, and ethics.
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  • (1 other version)Persistence.Christian Kanzian (ed.) - 2007 - Ontos.
    Preface The problem of persistence is as old as the tradition of systematic ontology: How can we explain that the middle-sized standard objects of ...
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  • Surrounding Space.Barry Smith & Achille C. Varzi - 2002 - Theory in Biosciences 121 (2):139-162.
    The history of evolution is a history of development from less to more complex organisms. This growth in complexity of organisms goes hand in hand with a concurrent growth in complexity of environments and of organism-environment relations. It is a concern with this latter aspect of evolutionary development that motivates the present paper. We begin by outlining a theory of organism-environment relations. We then show that the theory can be applied to a range of different sorts of cases, both biological (...)
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  • Concepts and Cognitive Science.Stephen Laurence & Eric Margolis - 1999 - In Eric Margolis & Stephen Laurence (eds.), Concepts: Core Readings. MIT Press. pp. 3-81.
    Given the fundamental role that concepts play in theories of cognition, philosophers and cognitive scientists have a common interest in concepts. Nonetheless, there is a great deal of controversy regarding what kinds of things concepts are, how they are structured, and how they are acquired. This chapter offers a detailed high-level overview and critical evaluation of the main theories of concepts and their motivations. Taking into account the various challenges that each theory faces, the chapter also presents a novel approach (...)
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  • (4 other versions)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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  • A Radical Solution to the Species Problem.Michael T. Ghiselin - 1974 - Systematic Zoology 23 (4):536–544.
    Traditionally, species have been treated as classes. In fact they may be considered individuals. The logical term “individual” has been confused with a biological synonym for “organism.” If species are individuals, then: 1) their names are proper, 2) there cannot be instances of them, 3) they do not have defining properties, 4) their constituent organisms are parts, not members. “ Species " may be defined as the most extensive units in the natural economy such that reproductive competition occurs among their (...)
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  • Parts of Classes.David K. Lewis - 1990 - Blackwell.
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  • Parts and Places: The Structures of Spatial Representation.Roberto Casati & Achille C. Varzi - 1999 - MIT Press.
    Thinking about space is thinking about spatial things. The table is on the carpet; hence the carpet is under the table. The vase is in the box; hence the box is not in the vase. But what does it mean for an object to be somewhere? How are objects tied to the space they occupy? This book is concerned with these and other fundamental issues in the philosophy of spatial representation. Our starting point is an analysis of the interplay between (...)
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  • The logical form of action sentences.Donald Davidson - 1966 - In Nicholas Rescher (ed.), The Logic of Decision and Action. University of Pittsburgh Press. pp. 81--95.
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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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  • 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 survey of metaphysics.E. Jonathan Lowe - 2002 - Oxford: Oxford University Press.
    A systematic overview of modern metaphysics, A Survey of Metaphysics covers all of the most important topics in the field. It adopts the fairly traditional conception of metaphysics as a subject that deals with the deepest questions that can be raised concerning the fundamental structure of reality as a whole. The book is divided into six main sections that address the following themes: identity and change, necessity and essence, causation, agency and events, space and time, and universals and particulars. It (...)
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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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  • Abstract particulars.Keith Campbell - 1990 - Cambridge, Mass., USA: Blackwell.
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  • The elements of being.Donald Cary Williams - 1953 - Review of Metaphysics 7 (2):3-18, 171-92.
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  • Relevance, relatedness and restricted set theory.Barry Smith - 1991 - In Georg Schurz (ed.), Advances in Scientific Philosophy. pp. 45-56.
    Relevance logic has become ontologically fertile. No longer is the idea of relevance restricted in its application to purely logical relations among propositions, for as Dunn has shown in his (1987), it is possible to extend the idea in such a way that we can distinguish also between relevant and irrelevant predications, as for example between “Reagan is tall” and “Reagan is such that Socrates is wise”. Dunn shows that we can exploit certain special properties of identity within the context (...)
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  • SNAP and SPAN: Towards dynamic spatial ontology.Pierre Grenon & Barry Smith - 2004 - Spatial Cognition and Computation 4 (1):69–103.
    We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the interconnections (...)
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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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  • The Logic of Biological Classification and the Foundations of Biomedical Ontology.Barry Smith - 2009 - In C. Glymour, D. Westerstahl & W. Wang (eds.), Logic, Methodology and Philosophy of Science. Proceedings of the 13th International Congress. King’s College. 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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  • Against Fantology.Barry Smith - 2005 - In Johann C. Marek Maria E. Reicher (ed.), Experience and Analysis. 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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  • Against idiosyncrasy in ontology development.Barry Smith - 2001 - In Barry Smith & Christopher Welty (eds.), Formal Ontology in Information Systems (FOIS). ACM Press. pp. 15-26.
    The world of ontology development is full of mysteries. Recently, ISO Standard 15926 (“Lifecycle Integration of Process Plant Data Including Oil and Gas Production Facilities”), a data model initially designed to support the integration and handover of large engineering artefacts, has been proposed by its principal custodian for general use as an upper level ontology. As we shall discover, ISO 15926 is, when examined in light of this proposal, marked by a series of quite astonishing defects, which may however provide (...)
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  • Beyond concepts: Ontology as reality representation.Barry Smith - 2001 - In Barry Smith & Christopher Welty (eds.), Formal Ontology in Information Systems (FOIS). ACM Press. pp. 1-12.
    The present essay is devoted to the application of ontology in support of research in the natural sciences. It defends the thesis that ontologies developed for such purposes should be understood as having as their subject matter, not concepts, but rather the universals and particulars which exist in reality and are captured in scientific laws. We outline the benefits of a view along these lines by showing how it yields rigorous formal definitions of the foundational relations used in many influential (...)
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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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  • Framework for formal ontology.Barry Smith & Kevin Mulligan - 1983 - Topoi 2 (1):73-85.
    The discussions which follow rest on a distinction, first expounded by Husserl, between formal logic and formal ontology. The former concerns itself with (formal) meaning-structures; the latter with formal structures amongst objects and their parts. The paper attempts to show how, when formal ontological considerations are brought into play, contemporary extensionalist theories of part and whole, and above all the mereology of Leniewski, can be generalised to embrace not only relations between concrete objects and object-pieces, but also relations between what (...)
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  • (1 other version)Fiat objects.Barry Smith - 2001 - Topoi 20 (2):131-148.
    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 cornucopia of formal-ontological relations.Barry Smith & Pierre Grenon - 2004 - Dialectica 58 (3):279–296.
    The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand four-dimensionalism.
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  • Truthmaker realism.Barry Smith - 1999 - Australasian Journal of Philosophy 77 (3):274 – 291.
    We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments are true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of (...)
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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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  • (1 other version)The problem of material constitution.Michael C. Rea - 1995 - Philosophical Review 104 (4):525-552.
    There are five individually plausible and jointly incompatible assumptions underlying four familiar puzzles about material constitution. The problem of material constitution just is the fact that these five assumptions are both plausible and incompatible. I will begin by providing a very general statement of the problem. I will present the five assumptions and provide a short argument showing how they conflict with one another. Then, in subsequent sections, I will go on to show how these assumptions underlie each of the (...)
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  • Naive action theory.Michael Thompson - 2008 - In Life and action: elementary structures of practice and practical thought. Cambridge: Harvard University Press.
    The question "Why?" that is deployed in these exchanges evidently bears the "special sense" Elizabeth Anscombe has linked to the concepts of intention and of a reason for action; it is the sort of question "Why?" that asks for what Donald Davidson later called a "rationalization".2 The special character of what is given, in each response, as formulating a reason ── a description, namely, of the agent as actually doing something, and, moreover, as..
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  • What is a species, and what is not?Ernst Mayr - 1996 - Philosophy of Science 63 (2):262-277.
    I analyze a number of widespread misconceptions concerning species. The species category, defined by a concept, denotes the rank of a species taxon in the Linnaean hierarchy. Biological species are reproducing isolated from each other, which protects the integrity of their genotypes. Degree of morphological difference is not an appropriate species definition. Unequal rates of evolution of different characters and lack of information on the mating potential of isolated populations are the major difficulties in the demarcation of species taxa.
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  • Functional anatomy: A taxonomic proposal.Ingvar Johansson, Barry Smith, Katherine Munn, Nikoloz Tsikolia, Kathleen Elsner, Dominikus Ernst & 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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  • The Ecological Approach to Visual Perception: Classic Edition.James J. Gibson - 1979 - Houghton Mifflin.
    This is a book about how we see: the environment around us (its surfaces, their layout, and their colors and textures); where we are in the environment; whether or not we are moving and, if we are, where we are going; what things are good for; how to do things (to thread a needle or drive an automobile); or why things look as they do.The basic assumption is that vision depends on the eye which is connected to the brain. The (...)
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  • The Human Animal: Personal Identity Without Psychology.Eric Todd Olson - 1997 - New York, US: Oxford University Press.
    Most philosophers writing about personal identity in recent years claim that what it takes for us to persist through time is a matter of psychology. In this groundbreaking new book, Eric Olson argues that such approaches face daunting problems, and he defends in their place a radically non-psychological account of personal identity. He defines human beings as biological organisms, and claims that no psychological relation is either sufficient or necessary for an organism to persist. Olson rejects several famous thought-experiments dealing (...)
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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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  • Language, Thought, and Other Biological Categories: New Foundations for Realism.Ruth Garrett Millikan - 1984 - MIT Press.
    Preface by Daniel C. Dennett Beginning with a general theory of function applied to body organs, behaviors, customs, and both inner and outer representations, ...
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  • (1 other version)The meaning of 'meaning'.Hilary Putnam - 1975 - Minnesota Studies in the Philosophy of Science 7:131-193.
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  • Ecological Psychology.Roger Barker - 1968 - Stanford University Press.
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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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  • (1 other version)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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