Ontology-Driven Method for Integrating Biomedical Repositories

  • José Antonio Miñarro-Giménez
  • Jesualdo Tomás Fernández-Breis
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7023)


Handling the increasing number of biological repositories and the growing amount of information they contain is a significant challenge for researchers. Thus, Semantic Web Technologies are the basis of the new approaches that are dealing with such challenges. In this paper, we describe a methodology to manage the integration of biomedical repositories into a knowledge base. This method is based on the explicit definition of the mappings between relational resources and the domain ontology and the conditions that determine the identity of a particular instance. We will describe both the method and its application to the OGO system which integrates orthologous genes and genetic diseases repositories into an ontological knowledge base.


Ontology-driven Integration Ontological Knowledge Base Biological repositories Orthologous Genes Genetic Diseases 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Galperin, M., Cochrane, G.: The 2011 nucleic acids research database issue and the online molecular biology database collection. Nucleic Acids Research Advance Access Nucl. Acids Res. 39, D1–D6 (2011)Google Scholar
  2. 2.
    NCBI: Ncbi entrez global search portal,
  3. 3.
    Uniprot Consortium: Ongoing and future developments at the universal protein resource. BMC Bioinformatics 39, 214–219 (2010)Google Scholar
  4. 4.
    Ashburner, M., Ball, C., Blake, J., Botstein, D., Butler, H., Cherry, J., Davis, A., Dolinski, K., Dwight, S., Eppig, J., Harris, M., Hill, D., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J., Richardson, J., Ringwald, M., Rubin, G., Sherlock, G.: Gene ontology: tool for the unification of biology. Nature Genetics 25, 25–29 (2000)CrossRefGoogle Scholar
  5. 5.
    Gruber, T.: Toward principles for the design of ontologies used for knowledge sharing. International Journal of Human-Computer Studies 43, 256–274 (1995)CrossRefGoogle Scholar
  6. 6.
    Bodenreider, O., Stevens, R.: Bio-ontologies: current trends and future directions. Briefings in Bioinformatics 7, 256–274 (2006)CrossRefGoogle Scholar
  7. 7.
    Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L., Eilbeck, K., Ireland, A., Mungall, C., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S., Scheuermann, R., Shah, N., Whetzel, P., Lewis, S.: The obo foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotech. 25(1087-0156), 1251–1255 (2007)CrossRefGoogle Scholar
  8. 8.
    Berners-Lee, T., Hendler, J., Lassila, O.: The semantic web. Scientific American 284(5), 34–43 (2001)CrossRefGoogle Scholar
  9. 9.
    RDF Working Group: Resource description framework,
  10. 10.
    W3C: Owl web ontology language,
  11. 11.
    W3C: Sparql query language for rdf,
  12. 12.
    Miñarro Giménez, J.A., Madrid, M., Fernández-Breis, J.T.: Ogo: an ontological approach for integrating knowledge about orthology. BMC Bioinformatics 10(S-10), 13 (2009)CrossRefGoogle Scholar
  13. 13.
    Fitch, W.M.: Distinguishing homologous from analogous proteins. Systematic Zoology 19(2), 99–113 (1970)MathSciNetCrossRefGoogle Scholar
  14. 14.
    Tatusov, R., Fedorova, N., Jackson, J., Jacobs, A., Kiryutin, B., Koonin, E., Krylov, D., Mazumder, R., Mekhedov, S., Nikolskaya, A., Rao, B., Smirnov, S., Sverdlov, A., Vasudevan, S., Wolf, Y., Yin, J., Natale, D.: The cog database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41+ (2003)Google Scholar
  15. 15.
    NCBI: Homologene database,
  16. 16.
    Chen, F., Mackey, A.J., Stoeckert Jr., C.J., Roos, D.S.: Orthomcl-db: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acid Research 34, 363–368 (2005)CrossRefGoogle Scholar
  17. 17.
    Remm, M., Storm, C., Sonnhammer, E.: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology 314(5), 1041–1052 (2001)CrossRefGoogle Scholar
  18. 18.
    NCBI: Omim database,
  19. 19.
    The Gene Ontology: Evidence codes ontology,
  20. 20.
  21. 21.
    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, R46 (2005)Google Scholar
  22. 22.
  23. 23.
    Guarino, N., Welty, C.: Evaluating ontological decisions with ontoclean. Communications of the ACM 45(2), 61–65 (2002)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • José Antonio Miñarro-Giménez
    • 1
  • Jesualdo Tomás Fernández-Breis
    • 1
  1. 1.Faculty of Computer ScienceUniversity of MurciaSpain

Personalised recommendations