Ontologies appliquées biomédicales et ontologie philosophique : un développement complémentaire
DOI:
https://doi.org/10.20416/lsrsps.v3i1.273Keywords:
ontologie appliquée, espèce naturelle, maladieAbstract
The massive increase of data generated by heterogeneous sources requires the development of computer tools enabling their semantic interoperability. Applied ontologies aim at fulfilling such needs. We will show in this article the central role that philosophical ontology can play for applied ontology, with a focus on biomedical ontologies; and reciprocally, how applied ontology can enlighten some classical issues in philosophical ontology, by considering the following question: Is disease a natural kind?
References
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ANGELELLI, Ignacio. 1991. Accidents III: The ontological square. In BURKHARDT, Hans, SMITH, Barry (dir). Handbook of metaphysics and ontology. Munich : Philosophia Verlag.
ANTONIOLI, Natalia, CASTANO, Francesco, COLETTA, Spartacco et al. 2014. Ontology based data management for the Italian public debt. In KUTZ, Oliver, GARBACZ, Pawel (dir.), Formal Ontology in Information Systems: Proceedings of the Eighth International Conference (FOIS 2014). Amsterdam : IOS Press. 372 385.
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BARTON, Adrien, ROVETTO, Robert, MIZOGUCHI, Riichiro. 2014. Newtonian Forces and causation: a dispositional account. In KUTZ, Oliver, GARBACZ, Pawel (dir.), Formal Ontology in Information Systems: Proceedings of the Eighth International Conference (FOIS 2014). Amsterdam : IOS Press. 157-170.
BARTON, Adrien, ROSIER, Arnaud, BURGUN, Anita, ETHIER, Jean-François. 2014. The cardiovascular disease ontology. In KUTZ, Oliver, GARBACZ, Pawel (dir.), Formal Ontology in Information Systems: Proceedings of the Eighth International Conference (FOIS 2014). Amsterdam : IOS Press. 409-414.
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CAMPBELL, Edward James Moran, SCADDING, John G. & ROBERTS, Robin S. 1979. The concept of disease. British Medical Journal, 2(6193), 757-762
CANUEL, Vincent, RANCE, Bastien, AVILLACH, Paul, et al. 2014. Translational research platforms integrating clinical and omics data: a review of publicly available solutions. Briefings in Bioinformatics, 1-11.
COOPER, Rachel. 2002. Disease. Studies in History and Philosophy of Biological and Biomedical Sciences, 33(2), 263-282.
COWELL, Lindsay G., SMITH, Barry. 2009. Infectious disease ontology. In SINTCHENKO, Vitali (dir.), Infectious Disease Informatics. New York : Springer. 373-395.
D’AMICO, Robert. 1995. Is disease a natural kind? Journal of Medicine and Philosophy, 20(5), 551–569.
DEVEDZIC, Vladan. 2004. Education and the semantic Web. International Journal of Artificial Intelligence in Education, 14(2), 165-191.
DRAGULINESCU, Stefan. 2010. Diseases as natural kinds. Theoretical Medicine and Bioethics, 31(5), 347-369.
GANGEMI, Aldo, GUARINO, Nicola, MASOLO, Claudio et al. 2002. Sweetening Ontologies with DOLCE. In GÓMEZ-PÉREZ, Asuncion, BENJAMINS, V. Richards (dir.), Knowledge engineering and knowledge management: Ontologies and the semantic Web, Lecture Notes in Computer Science. Berlin, Heidelberg : Springer. 166-181.
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JANSEN, Ludger. 2008. Categories: The top-level ontology. In MUNN, Katherine, SMITH, Barry (dir.), Applied ontology: an introduction. Francfort : Ontos-Verlag. 173-196.
JOHNSON, William. 1921. Logic: Part I. Cambridge : Cambridge University Press.
LEWIS, David. 1986. On the plurality of worlds. Oxford : Oxford University Press.
MARK, David M., SMITH, Barry, EGENHOFER, Max J., HIRTLE, Stephen C. 2004. Ontological foundations for geographic information science. In MCMASTER, Robert B., USERY, E. Lynn (dir.), A research agenda for geographic information science. Boca Raton : CRC Press. 335-350.
MASCARDI, Viviana, CORDÌ, Valentina, ROSSO, Paolo. 2006. A comparison of upper ontologies. WOA. 55-64.
MERRILL, Gary H. 2010. Ontological realism: Methodology or misdirection? Applied Ontology, 5(2), 79-108.
MIZOGUCHI, Riichiro, KOZAKI, Kouji, KOU, Hiroko, et al. 2011. River flow model of diseases. Proceedings of the 2nd International Conference on Biomedical Ontology (ICBO 2011). CEUR Workshop Proceedings. 63-70.
MUMFORD, Stephen. 1998. Dispositions. Oxford : Oxford University Press.
MURPHY, Dominic. 2009. Concepts of disease and health. ZALTA, Edward N. (dir.) The Stanford Encyclopedia of Philosophy (Summer 2009 Edition). Consulté le 19 janvier 2015 à http://plato.stanford.edu/archives/sum2009/entries/health-disease/
NOY, Natalya F., SHAH, Nigam H., WHETZEL, et al. 2009. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic acids research, 37(suppl 2), W170–W173.
REZNEK, Lawrie. 1987. The nature of disease. New York : Routledge & Kegan Paul.
REZNEK, Lawrie. 1995. Disease about kinds: reply to D’Amico. Journal of Medicine and Philosophy, 20(5), 571-584.
RÖHL, Jansennes, JANSEN, Ludger. 2011. Representing dispositions. Journal of Biomedical Semantics, 2(suppl 4), S4.
ROSSE, Cornelius, MEJINO José L. V. 2003. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. Journal of Biomedical Informatics, 36(6), 478-500.
SCHEUERMANN, Richard H., CEUSTERS, Werner, SMITH, Barry. 2009. Toward an ontological treatment of disease and diagnosis. Proceedings of the 2009 AMIA Summit on Translational Bioinformatics. San Francisco. 116-120.
SMITH, Barry. 2004. Beyond concepts: ontology as reality representation. In VARZI, Achille, VIEU, Laure (dir.), Formal Ontology in Information Systems: Proceedings of the third international conference (FOIS 2004). Amsterdam : IOS Press. 73–84.
SMITH, Barry (2005). Against Fantology. In MAREK, Johann Christian, REICHER, Maria Elisabeth (dir.), Experience and Analysis. Vienna : Öbv & Hpt. 153-170.
SMITH, Barry, ASHBURNER, Michael, ROSSE, Cornelius et al. 2007. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature biotechnology, 25(11), 1251–1255.
SMITH, Barry, CEUSTERS, Werner. 2010. Ontological realism: A methodology for coordinated evolution of scientific ontologies. Applied ontology, 5(3), 139–188.
WILLIAMS, Neil E. 2007. The factory model of disease. The Monist, 90(4), 555–584.
ANGELELLI, Ignacio. 1991. Accidents III: The ontological square. In BURKHARDT, Hans, SMITH, Barry (dir). Handbook of metaphysics and ontology. Munich : Philosophia Verlag.
ANTONIOLI, Natalia, CASTANO, Francesco, COLETTA, Spartacco et al. 2014. Ontology based data management for the Italian public debt. In KUTZ, Oliver, GARBACZ, Pawel (dir.), Formal Ontology in Information Systems: Proceedings of the Eighth International Conference (FOIS 2014). Amsterdam : IOS Press. 372 385.
ARMSTRONG, David Malet. 1980. A theory of universals, volume 2 : Universals and scientific realism. Cambridge : Cambridge University Press.
BARTON, Adrien, ROVETTO, Robert, MIZOGUCHI, Riichiro. 2014. Newtonian Forces and causation: a dispositional account. In KUTZ, Oliver, GARBACZ, Pawel (dir.), Formal Ontology in Information Systems: Proceedings of the Eighth International Conference (FOIS 2014). Amsterdam : IOS Press. 157-170.
BARTON, Adrien, ROSIER, Arnaud, BURGUN, Anita, ETHIER, Jean-François. 2014. The cardiovascular disease ontology. In KUTZ, Oliver, GARBACZ, Pawel (dir.), Formal Ontology in Information Systems: Proceedings of the Eighth International Conference (FOIS 2014). Amsterdam : IOS Press. 409-414.
BIRD, Alexander, TOBIN, Emma. 2012. Natural Kinds. In ZALTA, Edward N. (dir.), The Stanford Encyclopedia of Philosophy (Winter 2012 Edition). Consulté le 19 janvier 2015 à http://plato.stanford.edu/archives/win2012/entries/natural-kinds/
BOORSE, Christopher. 1977. Health as a Theoretical Concept. Philosophy of Science, 44(4), 542-573.
BURGUN, Anita, BODENREIDER, Olivier. 2008. Accessing and integrating data and knowledge for biomedical research. IMIA Yearbook of Medical Informatics, 3, 91 101.
CAMPBELL, Edward James Moran, SCADDING, John G. & ROBERTS, Robin S. 1979. The concept of disease. British Medical Journal, 2(6193), 757-762
CANUEL, Vincent, RANCE, Bastien, AVILLACH, Paul, et al. 2014. Translational research platforms integrating clinical and omics data: a review of publicly available solutions. Briefings in Bioinformatics, 1-11.
COOPER, Rachel. 2002. Disease. Studies in History and Philosophy of Biological and Biomedical Sciences, 33(2), 263-282.
COWELL, Lindsay G., SMITH, Barry. 2009. Infectious disease ontology. In SINTCHENKO, Vitali (dir.), Infectious Disease Informatics. New York : Springer. 373-395.
D’AMICO, Robert. 1995. Is disease a natural kind? Journal of Medicine and Philosophy, 20(5), 551–569.
DEVEDZIC, Vladan. 2004. Education and the semantic Web. International Journal of Artificial Intelligence in Education, 14(2), 165-191.
DRAGULINESCU, Stefan. 2010. Diseases as natural kinds. Theoretical Medicine and Bioethics, 31(5), 347-369.
GANGEMI, Aldo, GUARINO, Nicola, MASOLO, Claudio et al. 2002. Sweetening Ontologies with DOLCE. In GÓMEZ-PÉREZ, Asuncion, BENJAMINS, V. Richards (dir.), Knowledge engineering and knowledge management: Ontologies and the semantic Web, Lecture Notes in Computer Science. Berlin, Heidelberg : Springer. 166-181.
GRENON, Pierre, SMITH, Barry, Goldberg, Louis. 2004. Biodynamic ontology: applying BFO in the biomedical domain. Studies in health technology and informatics, 20 38.
VAN HARMELEN, Frank. 2005. Ontology mapping: a way out of the medical tower of Babel? Proceedings of the 10th Conference on Artificial Intelligence in Medicine, AIME’05. Berlin, Heidelberg : Springer. 3-6.
HAWLEY, Katherine. 2010. Temporal parts. In ZALTA, Edward N. (dir.), The Stanford Encyclopedia of Philosophy (Winter 2010 Edition). Consulté le 19 janvier 2015 à http://plato.stanford.edu/archives/win2010/entries/temporal-parts/
JANSEN, Ludger. 2008. Categories: The top-level ontology. In MUNN, Katherine, SMITH, Barry (dir.), Applied ontology: an introduction. Francfort : Ontos-Verlag. 173-196.
JOHNSON, William. 1921. Logic: Part I. Cambridge : Cambridge University Press.
LEWIS, David. 1986. On the plurality of worlds. Oxford : Oxford University Press.
MARK, David M., SMITH, Barry, EGENHOFER, Max J., HIRTLE, Stephen C. 2004. Ontological foundations for geographic information science. In MCMASTER, Robert B., USERY, E. Lynn (dir.), A research agenda for geographic information science. Boca Raton : CRC Press. 335-350.
MASCARDI, Viviana, CORDÌ, Valentina, ROSSO, Paolo. 2006. A comparison of upper ontologies. WOA. 55-64.
MERRILL, Gary H. 2010. Ontological realism: Methodology or misdirection? Applied Ontology, 5(2), 79-108.
MIZOGUCHI, Riichiro, KOZAKI, Kouji, KOU, Hiroko, et al. 2011. River flow model of diseases. Proceedings of the 2nd International Conference on Biomedical Ontology (ICBO 2011). CEUR Workshop Proceedings. 63-70.
MUMFORD, Stephen. 1998. Dispositions. Oxford : Oxford University Press.
MURPHY, Dominic. 2009. Concepts of disease and health. ZALTA, Edward N. (dir.) The Stanford Encyclopedia of Philosophy (Summer 2009 Edition). Consulté le 19 janvier 2015 à http://plato.stanford.edu/archives/sum2009/entries/health-disease/
NOY, Natalya F., SHAH, Nigam H., WHETZEL, et al. 2009. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic acids research, 37(suppl 2), W170–W173.
REZNEK, Lawrie. 1987. The nature of disease. New York : Routledge & Kegan Paul.
REZNEK, Lawrie. 1995. Disease about kinds: reply to D’Amico. Journal of Medicine and Philosophy, 20(5), 571-584.
RÖHL, Jansennes, JANSEN, Ludger. 2011. Representing dispositions. Journal of Biomedical Semantics, 2(suppl 4), S4.
ROSSE, Cornelius, MEJINO José L. V. 2003. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. Journal of Biomedical Informatics, 36(6), 478-500.
SCHEUERMANN, Richard H., CEUSTERS, Werner, SMITH, Barry. 2009. Toward an ontological treatment of disease and diagnosis. Proceedings of the 2009 AMIA Summit on Translational Bioinformatics. San Francisco. 116-120.
SMITH, Barry. 2004. Beyond concepts: ontology as reality representation. In VARZI, Achille, VIEU, Laure (dir.), Formal Ontology in Information Systems: Proceedings of the third international conference (FOIS 2004). Amsterdam : IOS Press. 73–84.
SMITH, Barry (2005). Against Fantology. In MAREK, Johann Christian, REICHER, Maria Elisabeth (dir.), Experience and Analysis. Vienna : Öbv & Hpt. 153-170.
SMITH, Barry, ASHBURNER, Michael, ROSSE, Cornelius et al. 2007. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature biotechnology, 25(11), 1251–1255.
SMITH, Barry, CEUSTERS, Werner. 2010. Ontological realism: A methodology for coordinated evolution of scientific ontologies. Applied ontology, 5(3), 139–188.
WILLIAMS, Neil E. 2007. The factory model of disease. The Monist, 90(4), 555–584.
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Published
2016-12-22
How to Cite
Barton, Adrien, and Rosier Arnaud. 2016. “Ontologies appliquées biomédicales Et Ontologie Philosophique : Un développement complémentaire”. Lato Sensu: Revue De La Société De Philosophie Des Sciences 3 (1). https://doi.org/10.20416/lsrsps.v3i1.273.
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Proceedings of the 2014 congress (metaphysics of science)
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