Metabolic Pathway Data and Application Integration

  • Ismael Navas-Delgado
  • Maria Jesús García-Godoy
  • José F. Aldana-Montes
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 157)

Abstract

This paper shows three previous approaches for data integration, Linked Data access and Web Service annotation, and what problems have to be solved in the context of Life Sciences to integrate and use Metabolic Pathway data published as Linked Data.

Keywords

Data Integration Link Data SPARQL Query Application Integration Natural Language Description 
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.
    Belleau, F., Nolin, M.A., Tourigny, N., Rigault, P., Morisette, J.: Bio2RDF: Towards a Mushup to Build Bioinformatics Knowledge Systems. J. Biomed. Inform. 41, 706–717 (2008), doi:10.1016/j.jbi.2008.03.004CrossRefGoogle Scholar
  2. 2.
    Momtchev, V., Peychev, D., Primov, T., Georgiev, G.: Expanding the Pathway and Interaction Knowledge in Linked Life Data. In: 8th Proceedings of International Semantic Web Challenge, October 25-29. EEUU, Washington (2008)Google Scholar
  3. 3.
    Risch, T., Josifovski, V.: Distibuted Data Integration through Object-Oriented Mediator Servers. Concurrency and Computation: Practice and Experience 13, 933–953 (2001), doi:10.1002/cpe.607MATHCrossRefGoogle Scholar
  4. 4.
    Tomasic, A., Amouroux, R., Bonnet, P., Kapitskaia, O., Naacke, H., Raschid, L.: The Distributed Information Search Component (Disco) and the World Wide Web. In: Proceedings of the 1997 ACM SIGMOD, pp. 546–548. ACM press (1997), doi:10.1.1.49.5405Google Scholar
  5. 5.
    Hammer, J., McHugh, J., Garcia-Molina, H.: Semistructured Data: The Tsimmis Experience. In: First East-European Workshop on Advances in Databases and Information Systems-ADBIS, St. Petersburg, Russia (1997), doi:10.1.1.136.465Google Scholar
  6. 6.
    Roth, T., Arya, M., Haas, L.M., Carey, M.J., Cody, W.F., Fagin, Schwarz, P.M., Thomas II, J., Wimmers, E.L.: The Garlic Project. In: SIGMOD Conference, p. 557 (1996)Google Scholar
  7. 7.
    Ksiezyk, T., Martin, G., Jia, Q.: InfoSleuth: Agent-Based System for Data Integration and Analysis. In: 25th Annual International Computer Software and Applications Conference, COMPSAC 2001, pp. 474–476 (2001), doi:10.1109/CMPSAC.2001.960655Google Scholar
  8. 8.
    Bergamaschi, S., Castano, S., Vincini, M., Beneventano, D.: Semantic integration of heterogeneous information sources. Data Knowl. Eng. 36, 215–224 (2001)MATHCrossRefGoogle Scholar
  9. 9.
    Bornhövd, C.: Semantic Metadata for the Integration of Web-Based Data for Electronic Commerce. In: International Conference on Advance Issues of E-Commerce and Web-Based Information Systems, WECWIS, pp. 137–145 (1999), doi:doi=10.1.1.24.9229Google Scholar
  10. 10.
    Mena, E., Kashyap, V., Sheth, A.P., Illarramendi, A.: OBSERVER: An Approach for Query Processing in Global Information Systems based on Interoperation across Pre-existing Ontologies. Distributed and Parallel Databases 8, 14–25 (1996), doi:10.1109/COOPIS.1996.554955Google Scholar
  11. 11.
    Cheung, K.H., Frost, H.R., Marshall, M.S., Prud’hommeaux, E., Samwald, M., Zhao, J., Paschke, A.: A journey to Semantic Web query federation in the life sciences. BMC Bioinformatics 10, 10 (2009), doi:10.1186/1471-2105-10-S10-S10CrossRefGoogle Scholar
  12. 12.
    Langegger, A.: Virtual data integration on the web: novel methods for accessing heterogeneous and distributed data with rich semantics. In: Proceedings of the 10th International Conference on Information Integration and Web-based Applications & Services, pp. 559–562. ACM, New York (2008), doi:10.1145/1497308.1497410Google Scholar
  13. 13.
    Huynh, D., Mazzocchi, S., Karger, D.R.: Piggy bank: Experience the Semantic Web inside your web browser. J. Web Sem. 5, 16–27 (2007), doi:10.1007/11574620_31CrossRefGoogle Scholar
  14. 14.
    Bishop, B., Kiryakov, A., Ognyanoff, D., Peikov, I., Tashev, Z., Velkov, R.: OWLIM: A family of scalable semantic repositories. Semantic Web 2, 33–42 (2011)CrossRefGoogle Scholar
  15. 15.
    Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M.: The KEGG Resource for Deciphering the Genome. Nucleic Acids Res. 32, 277–280 (2004), doi:10.1093/nar/gkh063CrossRefGoogle Scholar
  16. 16.
    Le Novère, N., Finney, A., Hucka, M., Bhalla, U.S., Champagne, F., Collado-Vides, F., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, L.J., Spence, H.D., Wanner, B.L.: Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 23, 1509–1515 (2005)CrossRefGoogle Scholar
  17. 17.
    Le Novère, N., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M.I., Wimalaratne, S.M., Bergman, F.T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villéger, A., Boyd, S.E., Calzone, L., Courtot, M., Dogrusoz, U., Freeman, T.C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D.B., Sander, C., Sauro, H., Snoep, J.L., Kohn, K., Kitano, H.: The Systems Biology Graphical Notation. Nat. Biotechnol. 27, 735–741 (2009)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Ismael Navas-Delgado
    • 1
  • Maria Jesús García-Godoy
    • 1
  • José F. Aldana-Montes
    • 1
  1. 1.Universidad de MálagaMálagaSpain

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