Advertisement

Bio2RDF Release 2: Improved Coverage, Interoperability and Provenance of Life Science Linked Data

  • Alison Callahan
  • José Cruz-Toledo
  • Peter Ansell
  • Michel Dumontier
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7882)

Abstract

Bio2RDF currently provides the largest network of Linked Data for the Life Sciences. Here, we describe a significant update to increase the overall quality of RDFized datasets generated from open scripts powered by an API to generate registry-validated IRIs, dataset provenance and metrics, SPARQL endpoints, downloadable RDF and database files. We demonstrate federated SPARQL queries within and across the Bio2RDF network, including semantic integration using the Semanticscience Integrated Ontology (SIO). This work forms a strong foundation for increased coverage and continuous integration of data in the life sciences.

Keywords

Semantic Web RDF Linked Data Life Sciences SPARQL 

References

  1. 1.
    Howe, D., Costanzo, M., Fey, P., Gojobori, T., Hannick, L., Hide, W., Hill, D.P., Kania, R., Schaeffer, M., St. Pierre, S., et al.: Big data: The future of biocuration. Nature 455(7209), 47–50 (2008)CrossRefGoogle Scholar
  2. 2.
    Goble, C., Stevens, R.: State of the nation in data integration for bioinformatics. J. Biomed. Inform. 41(5), 687–693 (2008)CrossRefGoogle Scholar
  3. 3.
    Cerami, E.G., Bader, G.D., Gross, B.E., Sander, C.: cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics 7, 497 (2006)CrossRefGoogle Scholar
  4. 4.
    Chen, H., Yu, T., Chen, J.Y.: Semantic Web meets Integrative Biology: a survey. Brief Bioinform. (2012)Google Scholar
  5. 5.
    Ruebenacker, O., Moraru, I.I., Schaff, J.C., Blinov, M.L.: Integrating BioPAX pathway knowledge with SBML models. IET Syst. Biol. 3(5), 317–328 (2009)CrossRefGoogle Scholar
  6. 6.
    Sansone, S.A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L., et al.: Toward interoperable bioscience data. Nat. Genet. 44(2), 121–126 (2012)CrossRefGoogle Scholar
  7. 7.
    Berlanga, R., Jimenez-Ruiz, E., Nebot, V.: Exploring and linking biomedical resources through multidimensional semantic spaces. BMC Bioinformatics 13(suppl. 1), S6 (2012)Google Scholar
  8. 8.
    Gennari, J.H., Neal, M.L., Galdzicki, M., Cook, D.L.: Multiple ontologies in action: composite annotations for biosimulation models. J. Biomed. Inform. 44(1), 146–154 (2011)CrossRefGoogle Scholar
  9. 9.
    Hoehndorf, R., Dumontier, M., Gennari, J.H., Wimalaratne, S., de Bono, B., Cook, D.L., Gkoutos, G.V.: Integrating systems biology models and biomedical ontologies. BMC Syst. Biol. 5, 124 (2011)CrossRefGoogle Scholar
  10. 10.
    Hoehndorf, R., Dumontier, M., Oellrich, A., Rebholz-Schuhmann, D., Schofield, P.N., Gkoutos, G.V.: Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. PLoS One 6(7), e22006 (2011)Google Scholar
  11. 11.
    Jonquet, C., Lependu, P., Falconer, S., Coulet, A., Noy, N.F., Musen, M.A., Shah, N.H.: NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources. Web Semant. 9(3), 316–324 (2011)CrossRefGoogle Scholar
  12. 12.
    Ruttenberg, A., Rees, J.A., Samwald, M., Marshall, M.S.: Life sciences on the Semantic Web: the Neurocommons and beyond. Brief Bioinform. 10(2), 193–204 (2009)CrossRefGoogle Scholar
  13. 13.
    Momtchev, V., Peychev, D., Primov, T., Georgiev, G.: Expanding the Pathway and Interaction Knowledge in Linked Life Data. In: Semantic Web Challenge: 2009, Amsterdam (2009)Google Scholar
  14. 14.
    Chen, B., Dong, X., Jiao, D., Wang, H., Zhu, Q., Ding, Y., Wild, D.J.: Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinformatics 11, 255 (2010)CrossRefGoogle Scholar
  15. 15.
    Campinas, S., Perry, T.E., Ceccarelli, D., Delbru, R., Tummarello, G.: Introducing RDF Graph Summary with Application to Assisted SPARQL Formulation, pp. 261–266 (2012)Google Scholar
  16. 16.
    Ansell, P.: Model and prototype for querying multiple linked scientific datasets. Future Generation Computer Systems 27(3), 329–333 (2011)CrossRefGoogle Scholar
  17. 17.
    Juty, N., Le Novere, N., Laibe, C.: Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res. 40(Database issue), D580–D586 (2012)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Alison Callahan
    • 1
  • José Cruz-Toledo
    • 1
  • Peter Ansell
    • 2
  • Michel Dumontier
    • 1
  1. 1.Department of BiologyCarleton UniversityOttawaCanada
  2. 2.eResearch Lab, School of ITEEUniversity of QueenslandBrisbaneAustralia

Personalised recommendations