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Function, role and disposition in Basic Formal Ontology

Proceedings of Bio-Ontologies Workshop, Intelligent Systems for Molecular Biology (ISMB), Toronto (2008)

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  1. 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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  • 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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  • Language, Thought, and Other Biological Categories.Ruth G. 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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  • Artifacts, Art Works, and Agency.Colin Lyas - 1993 - Journal of Aesthetics and Art Criticism 52 (3):367-369.
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  • What Functions Explain: Functional Explanation and Self-Reproducing Systems.Beth Preston - 2002 - Mind 111 (444):888-891.
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  • Evolution and Two Popular Proposals for the Definition of Function.Robert Arp - 2007 - Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 38 (1):19-30.
    In the biological realm, a complete explanation of a trait seems to include an explanation in terms of function. It is natural to ask of some trait, "What is its function?" or "What purpose in the organism does the particular trait serve?" or "What is the goal of its activity?" There are several views concerning the appropriate definition of function for biological matters. Two popular views of function with respect to living things are Cummins' organizational account and the Griffiths/Godfrey-Smith modern (...)
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  • Introduction.Roger Ariew & Peter Barker - 1990 - Synthese 83 (2):179-182.
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  • Tendencies and Other Realizables in Medical Information Sciences.Ludger Jansen - 2007 - The Monist 90 (4):534-554.
    In order to develop the ontology of tendencies for use in the representation of medical knowledge, tendencies are compared with other kinds of entities possessing the realizable-realization structure, specifically: dispositions, propensities, abilities and virtues. The peculiarities of tendencies are discussed and a standard schema of tendency ascription is developed in order to represent the relations between the ascriptions of tendency tokens to particulars and the ascriptions of tendency types to universals. Two nonstandard cases and their epistemic variants are discussed.
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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 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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  • 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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  • The Modern Philosophical Resurrection of Teleology.Mark Perlman - 2004 - The Monist 87 (1):3-51.
    Many objects in the world have functions. Typewriters are for typing. Can-openers are for opening cans. Lawnmowers are for cutting grass. That is what these things are for. Every day around the world people attribute functions to objects. Some of the objects with functions are organs or parts of living organisms. Hearts are for pumping blood. Eyes are for seeing. Countless works in biology explain the “Form, Function, and Evolution of... ” everything from bee dances to elephant tusks to pandas’ (...)
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  • Artifacts, Art Works, and Agency.Randall R. Dipert - 1993 - Temple University Press.
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  • Language, Thought, and Other Biological Categories.Ruth Garrett Millikan - 1984 - Behaviorism 14 (1):51-56.
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  • Gene Ontology Annotations: What They Mean and Where They Come From.P. Hill David, Barry Smith, S. McAndrews-Hill Monica & A. Blake Judith - 2008 - BMC Bioinformatics 9 (Suppl 5):S2.
    The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...)
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  • The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration.Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J. Mungall, Neocles Leontis & Others - 2007 - Nature Biotechnology 25 (11):1251--1255.
    The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...)
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  • Nature's Purposes: Analyses of Function and Design in Biology.Colin Allen, Marc Bekoff & George V. Lauder (eds.) - 1998 - MIT Press.
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  • What Functions Explain: Functional Explanation and Self-Reproducing Systems.Peter McLaughlin - 2000 - Cambridge University Press.
    This 2001 book offers an examination of functional explanation as it is used in biology and the social sciences, and focuses on the kinds of philosophical presuppositions that such explanations carry with them. It tackles such questions as: why are some things explained functionally while others are not? What do the functional explanations tell us about how these objects are conceptualized? What do we commit ourselves to when we give and take functional explanations in the life sciences and the social (...)
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