A Provenance Assisted Roadmap for Life Sciences Linked Open Data Cloud

  • Ali Hasnain
  • Qaiser Mehmood
  • Syeda Sana e Zainab
  • Stefan Decker
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 518)


A significant portion of Web of Data is composed of multiple datasets that add high value to biomedical research. These datasets have been exposed on the web as a part of the Life Sciences Linked Open Data (LSLOD) Cloud. Different initiatives have been proposed for navigating through these datasets with or without vocabulary reuse. The significance of provenance information regarding life sciences data is great as compared to any other domain. With the provenance information, user becomes aware regarding the source, size, format along with authorization and privilege associated with the data. Previously, we proposed an approach for the creation of an active Linked Life Sciences Data Roadmap, that catalogues and links concepts as well as properties from 137 public SPARQL endpoints. In this work we extend the Roadmap with the provenance information collected directly by querying datasets. We designed a set of queries and the results were catalouged. This extended Roadmap is useful for dynamically assembling queries for retrieving data along with the provenance from multiple SPARQL endpoints. We also demonstrate its use in conjunction with other tools for selective SPARQL querying and the visualization of the LSLOD cloud. We have evaluated the performance of our approach in terms of time taken and success rates of data retrieved.


Linked Data (LD) Provenance SPARQL Life Sciences (LS) Semantic web Query federation 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Baillie, C., Edwards, P., Pignotti, E.: Quality assessment, provenance, and the web of linked sensor data. In: Groth, P., Frew, J. (eds.) IPAW 2012. LNCS, vol. 7525, pp. 220–222. Springer, Heidelberg (2012) CrossRefGoogle Scholar
  2. 2.
    Bechhofer, S., Buchan, I., De Roure, D., Missier, P., et al.: Why linked data is not enough for scientists. Future Generation Computer Systems 29(2), 599–611 (2013)CrossRefGoogle Scholar
  3. 3.
    Buil-Aranda, C., Hogan, A., Umbrich, J., Vandenbussche, P.-Y.: SPARQL web-querying infrastructure: ready for action? In: Alani, H., et al. (eds.) ISWC 2013, Part II. LNCS, vol. 8219, pp. 277–293. Springer, Heidelberg (2013) CrossRefGoogle Scholar
  4. 4.
    Cheung, K.H., Frost, H.R., Marshall, M.S., et al.: A journey to semantic web query federation in the life sciences. BMC Bioinformatics 10(Suppl. 10), S10 (2009)CrossRefGoogle Scholar
  5. 5.
    Clark, K.G., Feigenbaum, L., Torres, E.: Sparql protocol for rdf. World Wide Web Consortium (W3C) Recommendation (2008)Google Scholar
  6. 6.
    Damásio, C.V., Analyti, A., Antoniou, G.: Provenance for SPARQL queries. In: Cudré-Mauroux, P., et al. (eds.) ISWC 2012, Part I. LNCS, vol. 7649, pp. 625–640. Springer, Heidelberg (2012) CrossRefGoogle Scholar
  7. 7.
    Dezani-Ciancaglini, M., Horne, R., Sassone, V.: Tracing where and who provenance in linked data: a calculus. Theoretical Computer Science 464, 113–129 (2012)zbMATHMathSciNetCrossRefGoogle Scholar
  8. 8.
    Goble, C., Stevens, R., Hull, D., et al.: Data curation+ process curation= data integration+ science. Briefings in Bioinformatics 9(6), 506–517 (2008)CrossRefGoogle Scholar
  9. 9.
    Hartig, O.: Trustworthiness of data on the web. In: Proceedings of the STI Berlin & CSW PhD Workshop. Citeseer (2008)Google Scholar
  10. 10.
    Hasnain, A., Fox, R., Decker, S., Deus, H.F.: Cataloguing and linking life sciences LOD cloud. In: 1st International Workshop on Ontology Engineering in a Data-driven World Collocated with EKAW 2012 (2012)Google Scholar
  11. 11.
    Hasnain, A., et al.: Linked biomedical dataspace: lessons learned integrating data for drug discovery. In: Mika, P., et al. (eds.) ISWC 2014, Part I. LNCS, vol. 8796, pp. 114–130. Springer, Heidelberg (2014) Google Scholar
  12. 12.
    Hasnain, A., et al.: A roadmap for navigating the life sciences linked open data cloud. In: Supnithi, T., Yamaguchi, T., Pan, J.Z., Wuwongse, V., Buranarach, M. (eds.) JIST 2014. LNCS, vol. 8943, pp. 97–112. Springer, Heidelberg (2015) CrossRefGoogle Scholar
  13. 13.
    Kamdar, M.R., Zeginis, D., Hasnain, A., Decker, S., Deus, H.F.: ReVeaLD: A user-driven domain-specific interactive search platform for biomedical research. Journal of Biomedical Informatics 47, 112–130 (2014)CrossRefGoogle Scholar
  14. 14.
    Lebo, T., Sahoo, S., McGuinness, D., Belhajjame, K., Cheney, J., Corsar, D., Garijo, D., Soiland-Reyes, S., Zednik, S., Zhao, J.: Prov-o: The prov ontology. W3C Recommendation, 30th April (2013)Google Scholar
  15. 15.
    Omitola, T., Zuo, L., Gutteridge, C., Millard, I.C., Glaser, H., Gibbins, N., Shadbolt, N.: Tracing the provenance of linked data using void. In: Proceedings of the International Conference on Web Intelligence, Mining and Semantics, p. 17. ACM (2011)Google Scholar
  16. 16.
    Paulheim, H., Hertling, S.: Discoverability of SPARQL endpoints in linked open data. In: ISWC (Posters & Demos), pp. 245–248 (2013)Google Scholar
  17. 17.
    Quackenbush, J.: Standardizing the standards. Molecular Systems Biology 2(1) (2006)Google Scholar
  18. 18.
    Stein, L.D.: Integrating biological databases. Nature Reviews Genetics 4(5), 337–345 (2003)CrossRefGoogle Scholar
  19. 19.
    Zeginis, D., et al.: A collaborative methodology for developing a semantic model for interlinking Cancer Chemoprevention linked-data sources. Semantic Web (2013)Google Scholar
  20. 20.
    Zhao, J., Miles, A., Klyne, G., Shotton, D.: Linked data and provenance in biological data webs. Briefings in Bioinformatics 10(2), 139–152 (2009)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Ali Hasnain
    • 1
  • Qaiser Mehmood
    • 1
  • Syeda Sana e Zainab
    • 1
  • Stefan Decker
    • 1
  1. 1.Insight Center for Data AnalyticsNational University of IrelandGalwayIreland

Personalised recommendations