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A Semantic Query Interface for the OGO Platform

  • José Antonio Miñarro-Giménez
  • Mikel Egaña Aranguren
  • Francisco García-Sánchez
  • Jesualdo Tomás Fernández-Breis
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6266)

Abstract

In the last years, a number of semantic biomedical systems have been developed to store biomedical knowledge in an accessible manner. However, their practical usage is limited, since they require expertise in semantic languages by the user, or, in the other hand, their query interfaces do not fully exploit the semantics of the knowledge represented. Such drawbacks were present in the OGO system, a resource that semantically integrates knowledge about orthologs and human genetic diseases, developed by our research group. In this paper, we present an extension of the OGO system for improving the process of designing advanced semantic queries. The query module requires the users to know and to manage only the OGO ontology, which represents the domain knowledge, simplifying the process of query building.

Keywords

Ontology Semantic Web Semantic Querying Biomedical Informatics 

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References

  1. 1.
    Berners-Lee, T., Hendler, J., Lassila, O.: The Semantic Web. Scientific American 284(5), 34–43 (2001)CrossRefGoogle Scholar
  2. 2.
    Bernstein, A., Kaufmann, E.: GINO - A Guided Input Natural Language Ontology Editor. In: Cruz, I., Decker, S., Allemang, D., Preist, C., Schwabe, D., Mika, P., Uschold, M., Aroyo, L.M. (eds.) ISWC 2006. LNCS, vol. 4273, pp. 144–157. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  3. 3.
    Bodenreider, O., Sahoo, S.S.: Semantic Web for Translational Biomedicine: Two Pilot Experiments. In: Proceedings of the AMIA Summit on Translational Bioinformatics, vol. 148 (2008)Google Scholar
  4. 4.
    Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R., Apweiler, R.: The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 32, D262–D266 (2004)Google Scholar
  5. 5.
    Jiménez-Ruiz, E., Berlanga, R., Nebot, V., Sanz, I.: OntoPath: A Language for Retrieving Ontology Fragments. In: Meersman, R., Tari, Z. (eds.) OTM 2007, Part I. LNCS, vol. 4803, pp. 897–914. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  6. 6.
    Miñarro Giménez, J., Madrid, M., Fernández-Breis, J.: OGO: an ontological approach for integrating knowledge about orthology. BMC Bioinformatics 10, S10–S13 (2009)Google Scholar
  7. 7.
    GO, C.: Gene Ontology: tool for the unification of biology. Nature Genetics 23, 25–29 (2000)Google Scholar
  8. 8.
    Namgoong, H., Kim, H.G.: Ontology-based Controlled Natural Language Editor Using CFG with Lexical Dependency. In: Aberer, K., Choi, K.-S., Noy, N., Allemang, D., Lee, K.-I., Nixon, L.J.B., Golbeck, J., Mika, P., Maynard, D., Mizoguchi, R., Schreiber, G., Cudré-Mauroux, P. (eds.) ASWC 2007 and ISWC 2007. LNCS, vol. 4825, pp. 351–364. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  9. 9.
    Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., Dicuccio, M., Federhen, S., Feolo, M., Helmberg, W., Geer, L., Kapustin, Y., Landsman, D., Lipman, D., Lu, Z., Madden, T., Madej, T., Maglott, D., Marchler-Bauer, A., Miller, V., Mizrachi, I., Ostell, J., Panchenko, A., Pruitt, K., Schuler, G., Sequeira, E., Sherry, S., Shumway, M., Sirotkin, K., Slotta, D., Souvorov, A., Starchenko, G., Tatusova, T., Wagner, L., Wang, Y., Wilbur, J., Yaschenko, E., Ye, J.: Database resources of the National Center for Biotechnology Information. Nucleic acids research (2009)Google Scholar
  10. 10.
    Schwitter, R.: A controlled natural language layer for the semantic web. In: Zhang, S., Jarvis, R.A. (eds.) AI 2005. LNCS (LNAI), vol. 3809, pp. 425–434. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  11. 11.
    Smart, P.: Controlled natural languages and the semantic web. Tech. rep., School of Electronics and Computer Science, University of Southampton, Technical Report ITA/P12/SemWebCNL (2008)Google Scholar
  12. 12.
    Smith, B., Ceusters, W., Klagges, B., Kohler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A., Rosse, C.: Relations in Biomedical Ontologies. Genome Biology 6, R:46 (2005)Google Scholar
  13. 13.
    Valencia-García, R., García-Sánchez, F., Castellanos-Nieves, D., Fernández-Breis, J.: OWLPath: An OWL Ontology-Guided Query Editor. IEEE Transactions on Systems, Man, and Cybernetics - Part A: Systems and Humans (2010), doi:10.1109/TSMCA.2010.2048029Google Scholar
  14. 14.
    Wang, C., Xiong, M., Zhou, Q., Yu, Y.: PANTO: A Portable Natural Language Interface to Ontologies. In: Franconi, E., Kifer, M., May, W. (eds.) ESWC 2007. LNCS, vol. 4519, pp. 473–487. Springer, Heidelberg (2007)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • José Antonio Miñarro-Giménez
    • 1
  • Mikel Egaña Aranguren
    • 1
  • Francisco García-Sánchez
    • 1
  • Jesualdo Tomás Fernández-Breis
    • 1
  1. 1.Facultad de InformáticaUniversidad de MurciaMurciaSpain

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