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An Approach to Automatic Ontology-Based Annotation of Biomedical Texts

  • Gayo Diallo
  • Michel Simonet
  • Ana Simonet
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4031)

Abstract

Sharing and enriching of documents is expected and is made possible nowadays with tools enabling users to perform different kinds of annotations. We propose an Ontology-based approach to automate the semantic annotation of texts; Ontologies are represented in OWL (Web Ontology Language). OWL is supported by Semantic Web tools such as Racer for reasoning purpose and Jena. The tool for automatic semantic annotation supporting word-based and stem-based pre-indexing techniques is presented and its evaluation is made on three medical corpora both in English and French (brain disease area, cardiology and OHSUMED collection). The evaluation shows difference in the results obtained according to the pre-indixng mode used.

Keywords

Domain Ontology Semantic Annotation Prefer Term Biomedical Text Anatomical Ontology 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Berners-Lee, T., Hendler, J., Lassila, O.: Semantic web. Scientific American 1(1), 68–88 (2000)Google Scholar
  2. 2.
    Hillmann, D.: Guide d’utilisation du Dublin Core, consulted on (11/29/2005), http://www.bibl.ulaval.ca/DublinCore/usageguide-20000716fr.htm
  3. 3.
    Patriarche, R., Gedzelman, S., Diallo, G., Bernhard, D., Bassolet, C.G., Ferriol, S., Girard, A., Mouries, M., Palmer, P., Simonet, A., Simonet, M.: A Tool for Conceptual and Textual Annotation of Documents. In: e-challenges conference, Ljubljana, October 19-21 (2005)Google Scholar
  4. 4.
    Kahan, J., Koivunen, M.R., Prud’Hommeaux, E., Swick, R.: Annotea: an open RDF Infrastructure for Shared Web Annotations. In: Proceedings of WWW 2001, Hong-Kong, May 1-5, pp. 623–632 (2001)Google Scholar
  5. 5.
    Dill, S., Eiron, N., Gibson, D., Gruhl, D., Guha, R., Jhingran, A., Kanungo, T., Rajagopalan, S., Tomkins, A., Tomlin, J.A., Zien, J.Y.: SemTag and Seeker: Bootstrapping the Semantic Web via Automated Semantic Annotation. In: Proceedings International WWW Conference, Budapest, Hungary (2003)Google Scholar
  6. 6.
    Caussanel, J.P., Cahier, J.P., Zacklad, M., Charlet, J.: Les Topic Maps sont-ils un bon candidat pour l’ingénierie du Web Sémantique? In: Proceedings of IC 2002, Rouen (June 2002)Google Scholar
  7. 7.
    Ciravegna, F., Dingli, A., Petrelli, D., Wilks, Y.: User-system cooperation in document annotation based on information extraction. In: Gómez-Pérez, A., Benjamins, V.R. (eds.) EKAW 2002. LNCS, vol. 2473, p. 122. Springer, Heidelberg (2002)CrossRefGoogle Scholar
  8. 8.
    Handschuh, S., Staab, S., Ciravegna, F.: S-Cream, Semi-Automatic Creation of Metadata. In: Gómez-Pérez, A., Benjamins, V.R. (eds.) EKAW 2002. LNCS, vol. 2473, p. 358. Springer, Heidelberg (2002)CrossRefGoogle Scholar
  9. 9.
    Heflin, J., Hendler, J.: Searching the web with shoe. In: Artifial Intelligence for Web Search, pp. 35–40. AAAI Press, Menlo Park (2000)Google Scholar
  10. 10.
    Gandon, F.: Agents handling annotation distribution in a corporate semantic Web. In: Liu, J., Zhong, N. (eds.) Web Intelligence and Agent Systems, IOS Press, Amsterdam; International Journal 1(1), 23–45(2003) ISSN: 1570-1263 WI ConsortiumGoogle Scholar
  11. 11.
    Gruber, T.R.: A translation approach to portable ontologies. Knowledge Acquisition 5(2), 199–220 (1993)CrossRefGoogle Scholar
  12. 12.
    Diallo, G., Simonet, M., Simonet, A.: Bringing Together Structured and Unstructured Sources. In: DEXA 2006. Krakow, Poland (paper submitted)Google Scholar
  13. 13.
    Carroll, J.J., Dickinson, I., Dollin, C., Reynolds, D., Seaborne, A., Wilkinson, K.: Jena: implementing the semantic web recommendations. In: Proceedings of the 13th International World Wide Web Conference, New York, pp. 74–83 (2004)Google Scholar
  14. 14.
    Gedzelman, S., Simonet, M., Bernhard, D., Diallo, G., Palmer, P.: Building an Ontology of Cardio-Vascular Diseases for Concept-Based Information Retrieval. Computer in Cardiology, Lyon-France (2005)Google Scholar
  15. 15.
    SKOS: Schema for Knowledge Organisation Systems, http://www.w3.org/TR/2005/WD-swbp-skos-core-guide-20050510/
  16. 16.
    Lassila, O., Swick, R.: Ressource Description Framework (RDF) model and syntax specification. W3C Working Draft (1998), http://www.w3.org/TR/WD-rdf-syntax
  17. 17.
    Diallo, G., Bernhard, D., Batrancourt, B., Simonet, M.: Vers une Ontologie anatomo-fonctionnelle du cerveau, Journée Web Sémantique Médicale, Rennes (2003)Google Scholar
  18. 18.
    Haarslev, V., Möller, R.: Racer: A Core Inference Engine for the Semantic Web. In: Fensel, D., Sycara, K.P., Mylopoulos, J. (eds.) ISWC 2003. LNCS, vol. 2870, pp. 27–36. Springer, Heidelberg (2003)Google Scholar
  19. 19.
    Salton, G., Buckley, C.: Term-weighting approaches in automatic text retrieval. Information Processing and Management 24(5), 513–523 (1998)CrossRefGoogle Scholar
  20. 20.
    Batrancourt, B.: Modélisation et outils logiciels pour une connaissance anatomo-fonctionnelle du cerveau humain. Thèse de Doctorat, Université Lyon (December 1, 2003)Google Scholar
  21. 21.
    Kraaij, W., Pohlmann, R.: Viewing stemming as recall enhancement. In: Proc. of SIGIR 1996, Zurich, Switzerland, pp. 40–48 (1996)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Gayo Diallo
    • 1
  • Michel Simonet
    • 1
  • Ana Simonet
    • 1
  1. 1.Laboratoire TIMCUniversité Grenoble 1, Faculté de MédecineLa TroncheFrance

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