Abstract
Representing the Foundational Model of Anatomy (FMA) in OWL 2 is essential for semantic interoperability. The paper describes the method and tool used to formalize the FMA in OWL 2. One main strength of the approach is to leverage OWL 2 expressiveness and the naming conventions of the native FMA to make explicit some implicit semantics, meanwhile improving its ontological model and fixing some errors. A second originality is the flexible tool developed. It enables to easily generate a new version for each Protégé FMA update. While it provides one ‘standard’ FMA-OWL version by default, many options allow for producing other variants customized to users applications. To the best of our knowledge, no complete representation of the entire FMA in OWL DL or OWL 2 existed so far.
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References
Rosse, C., Mejino Jr, J.L.: The Foundational Model of Anatomy Ontology. In: Burger, A., et al. (eds.) Anatomy Ontologies for Bioinformatics: Principles and Practice, pp. 59–118. Springer, New York (2008) ISBN 978-1-84628-884-5
Rosse, C., Mejino Jr, J.L.: A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed. Inform. 36(6), 478–500 (2003)
Golbreich, C., Zhang, S., Bodenreider, O.: The Foundational Model of Anatomy in OWL: experience and perspectives. Journal of Web Semantics, Web Semantics: Science, Services and Agents on the World Wide Web 4(3), 181–195 (2006)
Dameron, O., Rubin, D.L., Musen, M.A.: Challenges in converting frame based ontology into OWL: the Foundational Model of Anatomy case-study. In: AMIA Annual Symposium, Washington DC, pp. 181–185 (2005)
Natalya, F., Noy, D.L.: Rubin, Translating the Foundational Model of Anatomy into OWL. Journal of Web Semantics, Web Semantics: Science, Services and Agents on the World Wide Web 6, 133–136 (2008)
Dameron, O., Chabalier, J.: Automatic generation of consistency constraints for an OWL representation of the FMA. In: 10th International Protégé Conference (2007)
Glimm, B., Horrocks, I., Motik, B.: Optimized Description Logic Reasoning via Core Blocking. In: Giesl, J., Hähnle, R. (eds.) IJCAR 2010. LNCS, vol. 6173, pp. 457–471. Springer, Heidelberg (2010)
W3C, O.W.L., Working Group, O.W.L.: 2 Web Ontology Language Document Overview W3C Recommendation October 27 (2009), http://www.w3.org/TR/owl2-overview/
Golbreich, C., Wallace, E.K.: OWL 2 Web Ontology Language New Features and Rationale W3C Recommendation October 27 (2009), http://www.w3.org/TR/owl2-new-features/
Darmoni, S.J., Pereira, S., Névéol, A., Massari, P., Dahamna, B., Letord, C., Kedelhué, G., Piot, J., Derville, A., Thirion, B.: French Infobutton: an academic and business perspective. In: AMIA Symp., p. 920. IOS Press, Amsterdam (2008)
Mikroyannidi, E., Rector, A., Stevens, R.: Abstracting and Generalizing the Foundationql Model of Anatomy ontology. In: Bio-ontologies 2009 (2009)
Motik, B., et al.: Representing Ontologies Using Description Logics, Description Graphs, and Rules. Artificial Intelligence 173(14), 1275–1309 (2009)
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Golbreich, C., Grosjean, J., Darmoni, S.J. (2011). The FMA in OWL 2. In: Peleg, M., Lavrač, N., Combi, C. (eds) Artificial Intelligence in Medicine. AIME 2011. Lecture Notes in Computer Science(), vol 6747. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-22218-4_25
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DOI: https://doi.org/10.1007/978-3-642-22218-4_25
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