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  1. 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 Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics 2994). Berlin: 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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  • Controlled vocabularies in bioinformatics: A case study in the Gene Ontology.Barry Smith & Anand Kumar - 2004 - Drug Discovery Today: Biosilico 2 (6):246-252.
    The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring the (...)
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  • Analytic Metaphysics versus Naturalized Metaphysics: The Relevance of Applied Ontology.Baptiste Le Bihan & Adrien Barton - 2021 - Erkenntnis 86 (1):21-37.
    The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel by French (...)
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  • Natural necessity: An introductory guide for ontologists.Fumiaki Toyoshima - forthcoming - Applied ontology:1-29.
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  • Functions in Basic Formal Ontology.Andrew D. Spear, Werner Ceusters & Barry Smith - 2016 - Applied ontology 11 (2):103-128.
    The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...)
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  • In defense of proper functions.Ruth Garrett Millikan - 1989 - Philosophy of Science 56 (June):288-302.
    I defend the historical definition of "function" originally given in my Language, Thought and Other Biological Categories (1984a). The definition was not offered in the spirit of conceptual analysis but is more akin to a theoretical definition of "function". A major theme is that nonhistorical analyses of "function" fail to deal adequately with items that are not capable of performing their functions.
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  • Ontology, Ontologies, and Science.Gary H. Merrill - 2011 - Topoi (1):71-83.
    Philosophers frequently struggle with the relation of metaphysics to the everyday world, with its practical value, and with its relation to empirical science. This paper distinguishes several different models of the relation between philosophical ontology and applied (scientific) ontology that have been advanced in the history of philosopy. Adoption of a strong participation model for the philosophical ontologist in science is urged, and requirements and consequences of the participation model are explored. This approach provides both a principled view and justification (...)
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  • Functions, Malfunctioning, and Negative Causation.Ludger Jansen - 2018 - In Antonio Piccolomini D’Aragona, Martin Carrier, Roger Deulofeu, Axel Gelfert, Jens Harbecke, Paul Hoyningen-Huene, Lara Huber, Peter Hucklenbroich, Ludger Jansen, Elizaveta Kostrova, Keizo Matsubara, Anne Sophie Meincke, Andrea Reichenberger, Kian Salimkhani & Javier Suárez (eds.), Philosophy of Science: Between the Natural Sciences, the Social Sciences, and the Humanities. Springer Verlag. pp. 117-135.
    Functional explanations apply not only in cases of normal functioning, but also in the case of malfunctioning. According to a straightforward analysis, a bearer of the function to F is malfunctioning if and only if it does not F although it should do so. This makes malfunctions and malfunctionings analogous to negative causation and thus peculiarly problematic, because they seem to involve absent dispositions and absent processes. This analysis seems also to require that the function to F cannot be identical (...)
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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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  • Biomedical Ontologies.Barry Smith - forthcoming - In Peter Elkin (ed.), Terminology, Ontology and their Implementations. Springer Nature Switzerland AG.
    We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...)
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  • Logical Investigations.Edmund Husserl - 1970 - London, England: Routledge.
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  • Bridging mainstream and formal ontology: A causality-based upper ontology in Dietrich of Freiberg.Luis M. Augusto - 2021 - Journal of Knowledge Structures and Systems 2 (2):35.
    Ontologies are some of the most central constructs in today's large plethora of knowledge technologies, namely in the context of the semantic web. As their coinage indicates, they are direct heirs to the ontological investigations in the long Western philosophical tradition, but it is not easy to make bridges between them. Contemporary ontological commitments often take causality as a central aspect for the ur-segregation of entities, especially in scientific upper ontologies; theories of causality and philosophical ontological investigations often go hand-in-hand, (...)
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  • Objects and their environments: From Aristotle to ecological ontology.Barry Smith - 2001 - In Andrew U. Frank, Jonathan Raper & Jean-Paul Cheylan (eds.), The Life and Motion of Socio-Economic Units. London: Taylor & Francis. pp. 79-97.
    What follows is a contribution to the theory of space and of spatial objects. It takes as its starting point the philosophical subfield of ontology, which can be defined as the science of what is: of the various types and categories of objects and relations in all realms of being. More specifically, it begins with ideas set forth by Aristotle in his Categories and Metaphysics, two works which constitute the first great contributions to ontological science. Because Aristotle’s ontological ideas were (...)
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  • Individuals, universals, collections: On the foundational relations of ontology.Thomas Bittner, Maureen Donnelly & Barry Smith - 2004 - In Achille Varzi Laure Vieu (ed.), ”, Formal Ontology in Information Systems. Proceedings of the Third International Conference. Amsterdam: IOS Press. pp. 37–48.
    This paper provides an axiomatic formalization of a theory of foundational relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the is-a relation among universals and the part-of relation among individuals as well as cross-category relations such as instance-of, member-of, and partition-of. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical (...)
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  • Ontology (Science).Barry Smith - 2008 - In Carola Eschenbach & Mike Grüninger (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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  • Gene Ontology: Tool for the unification of biology.M. Ashburner - 2000 - Nature Genetics 25:25-29.
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  • Ontology as Product-Service System: Lessons Learned from GO, BFO and DOLCE.Barry Smith - 2019 - In Proceedings of the 10th International Conference on Biomedical Ontology (ICBO), Buffalo, NY.
    This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The paper provides a detailed (...)
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