OpenFlyData: The Way to Go for Biological Data Integration

  • Jun Zhao
  • Alistair Miles
  • Graham Klyne
  • David Shotton
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5647)

Abstract

Although many applications have attempted to provide integrative access to distributed datasets, domain scientists largely continue to harvest research data in a conventional way, by consulting each resource independently, because such applications do not fully meet users’ needs. This paper describes OpenFlyData (http://openflydata.org/), a simple user-led service providing Drosophila researchers with integrated access to distributed information. This is an exemplar lightweight solution to the problems of data integration, in which accurate and explicit data modelling enables high precision information retrieval.

Keywords

data integration user-led life science semantic web 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Belleau, F., Nolin, M., Tourigny, N., Rigault, P., Morissette, J.: Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics 41, 706–716 (2008)CrossRefPubMedGoogle Scholar
  2. 2.
    Benson, E., Klyne, G., Gudmannsdottir, E., Shotton, D., White-Cooper, H.: The Drosophila testis gene expression database. In: The 47th Annual Drosophila Research Conference (2006)Google Scholar
  3. 3.
    Bizer, C., Cyganiak, R.: D2R Server–publishing relational databases on the semantic web (poster). In: Proceedings of the 5th International Semantic Web Conference, Athens, GA, USA (2006)Google Scholar
  4. 4.
    Chintapalli, V., Wang, J., Dow, J.: Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nature Genetics 39(6), 715 (2007)CrossRefPubMedGoogle Scholar
  5. 5.
    Clark, K.G., Feigenbaum, L., Torres, E.: SPARQL protocol for RDF (2008), http://www.w3.org/TR/rdf-sparql-protocol/
  6. 6.
    Goble, C., Stevens, R.: State of the nation in data integration for bioinformatics. Journal of Biomedical Informatics 41(5), 687–693 (2008)CrossRefPubMedGoogle Scholar
  7. 7.
    Jiang, J., White-Cooper, H.: Transcriptional activation in Drosophila spermatogenesis involves the mutually dependent function of aly and a novel meiotic arrest gene cookie monste. Development 130, 563–573 (2008)CrossRefGoogle Scholar
  8. 8.
    Lyne, R., Smith, R., Rutherford, K., Wakeling, M., Varley, A., Guillier, F., Janssens, H., Ji, W., McLaren, P., North, P., et al.: FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biology 8(7), R129 (2007)CrossRefGoogle Scholar
  9. 9.
    Oinn, T., Greenwood, M., Addis, M., Alpdemir, M.N., Ferris, J., Glover, K., Goble, C., Goderis, A., Hull, D., Marvin, D., Li, P., Lord, P., Pocock, M.R., Senger, M., Stevens, R., Wipat, A., Wroe, C.: Taverna: Lessons in creating a workflow environment. Concurrency and Computation: Practice and Experience 18(10), 1067–1100 (2006)CrossRefGoogle Scholar
  10. 10.
    Phuoc, D.L., Polleres, A., Tummarello, G., Morbidoni, C., Hauswirth, M.: Rapid Semantic Web mashup development through Semantic Web Pipes. In: Proceeding of the 18th International World Wide Web Confernce, Madrid, Spain (2009) (to appear)Google Scholar
  11. 11.
    Prud’hommeaux, E., Seaborne, A.: SPARQL query language for RDF (2008), http://www.w3.org/TR/rdf-sparql-query/
  12. 12.
    Stein, L.: Integrating biological databases. Nature Reviews Genetics 4(5), 337–345 (2003)CrossRefPubMedGoogle Scholar
  13. 13.
    Stein, L.: Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nature Reviews Genetics 9(9), 678–688 (2008)CrossRefPubMedGoogle Scholar
  14. 14.
    Tomancak, P., Beaton, A., Weiszmann, R., Kwan, E., Shu, S., Lewis, S.E., Richards, S., Ashburner, M., Hartenstein, V., Celniker, S.E., Rubin, G.M.: Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biology 3(12), 81–88 (2002)CrossRefGoogle Scholar
  15. 15.
    Tweedie, S., Ashburner, M., Falls, K., Leyland, P., McQuilton, P., Marygold, S., Millburn, G., Osumi-Sutherland, D., Schroeder, A., Seal, R., Zhang, H.: The FlyBase Consortium. FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Research 37, 5555–5559 (2009)CrossRefGoogle Scholar
  16. 16.
    Van de Sompel, H., Nelson, M., Lagoze, C., Warner, S.: Resource harvesting within the OAI-PMH framework. D-Lib Magazine 10(12), 1082–9873 (2004)Google Scholar
  17. 17.
    Wilkinson, M., Links, M.: BioMOBY: An open source biological web services proposal. Briefings in Bioinformatics 3(4), 331–341 (2002)CrossRefPubMedGoogle Scholar
  18. 18.
    Zhao, J., Klyne, G., Shotton, D.: Building a Semantic Web image repository for biological research images. In: Bechhofer, S., Hauswirth, M., Hoffmann, J., Koubarakis, M. (eds.) ESWC 2008. LNCS, vol. 5021, pp. 154–169. Springer, Heidelberg (2008)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Jun Zhao
    • 1
  • Alistair Miles
    • 1
  • Graham Klyne
    • 1
  • David Shotton
    • 1
  1. 1.Department of ZoologyUniversity of OxfordOxfordUK

Personalised recommendations