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The Relevance of Philosophical Ontology to Information and Computer Science

In Ruth Hagenbruger & Uwe V. Riss (eds.), Philosophy, computing and information science. Pickering & Chattoo. pp. 75-83 (2014)

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  1. Strengths and Limitations of Formal Ontologies in the Biomedical Domain.Barry Smith - 2009 - Electronic Journal of Communication, Information and Innovation in Health 3 (1):31-45.
    We propose a typology of representational artifacts for health care and life sciences domains and associate this typology with different kinds of formal ontology and logic, drawing conclusions as to the strengths and limitations for ontology in a description logics framework. The four types of domain representation we consider are: (i) lexico-semantic representation, (ii) representation of types of entities, (iii) representations of background knowledge, and (iv) representation of individuals. We advocate a clear distinction of the four kinds of representation in (...)
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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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  • (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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  • (6 other versions)Ontology (Science).Barry Smith - 2008 - In Carola Eschenbach & Michael Gruninger (eds.), Formal Ontology in Information Systems. Proceedings of the Fifth International Conference (FOIS 2008). Amsterdam: IOS Press. pp. 21-35.
    Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find self-evident) (...)
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  • The Second Naive Physics Manifesto.P. J. Hayes - 1985 - In Jerry R. Hobbs & Robert C. Moore (eds.), Formal Theories of the Commonsense World. Intellect Books.
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  • Circumscription — A Form of Non-Monotonic Reasoning.John McCarthy - 1980 - Artificial Intelligence 13 (1-2):27–39.
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  • Adapting Clinical Ontologies in Real-World Environments.Holger Stenzhorn, Stefan Schulz, Martin Boeker & Barry Smith - 2008 - Journal of Universal Computer Science 14 (22):3767-3780.
    The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...)
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  • Gene Ontology: Tool for the unification of biology.M. Ashburner - 2000 - Nature Genetics 25:25-29.
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  • (1 other version)Symposium: On What there is.P. T. Geach, A. J. Ayer & W. V. Quine - 1948 - Aristotelian Society Supplementary Volume 25 (1):125-160.
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  • Promisings and Other Social Acts: Their Constituents and Structure.Kevin Mulligan - 1987 - In Speech Act and Sachverhalt: Reinach and the Foundations of Realist Phenomenology. Reidel.
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