An Event-Driven Architecture for Biomedical Data Integration and Interoperability

  • Pedro Lopes
  • José Luís Oliveira
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9044)


Connecting data and services is nowadays an essential skill for life sciences researchers. Handling data from unrelated sources using problem-specific software or labor-intensive tools are common tasks. Despite the latest advances, integration and interoperability developments still involve primitive interactions and manual triggers. On the one hand, available tools cover specific niches, ignoring more generic problems. On the other hand, overly complex tools with excessive features dominate the market. In this proposal we introduce a cloud-based architecture to simplify real-time integration and interoperability for biomedical data. We support our strategy in an event-driven service-oriented architecture, where new data are pushed from any content source, through an intelligent proxy, for delivery to heterogeneous endpoints. This enables a passive integration approach, providing developers with a streamlined solution for deploying integrative biomedical applications.


Distributed/Internet based software engineering tools and techniques interoperability data translation data warehouse and repository bioinformatics 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Sascha, S., Kurtz, S.: A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9, 345–357 (2012)CrossRefGoogle Scholar
  2. 2.
    Thiam Yui, C., Liang, L.J., Jik Soon, W., Husain, W.: A Survey on Data Integration in Bioinformatics. In: Abd Manaf, A., Sahibuddin, S., Ahmad, R., Mohd Daud, S., El-Qawasmeh, E. (eds.) ICIEIS 2011, Part IV. CCIS, vol. 254, pp. 16–28. Springer, Heidelberg (2011)CrossRefGoogle Scholar
  3. 3.
    Darmont, J., Boussaid, O., Ralaivao, J.-C., Aouiche, K.: An architecture framework for complex data warehouses. arXiv preprint arXiv:0707.1534 (2007)Google Scholar
  4. 4.
  5. 5.
    Goble, C., Stevens, R.: State of the nation in data integration for bioinformatics. Journal of Biomedical Informatics 41, 687–693 (2008)CrossRefGoogle Scholar
  6. 6.
    Dudley, J.T., Butte, A.J.: Reproducible in silico research in the era of cloud computing. Nature Biotechnology 28, 1181 (2010)CrossRefGoogle Scholar
  7. 7.
    Schönherr, S., Forer, L., Weißensteiner, H., Kronenberg, F., Specht, G., Kloss-Brandstätter, A.: Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds. BMC Bioinformatics 13, 200 (2012)CrossRefGoogle Scholar
  8. 8.
    Sansone, S.-A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L.: Toward interoperable bioscience data. Nature Genetics 44, 121–126 (2012)CrossRefGoogle Scholar
  9. 9.
    Jamil, H.M.: Designing Integrated Computational Biology Pipelines Visually. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10, 605–618 (2013)CrossRefGoogle Scholar
  10. 10.
    Hunter, A., Macgregor, A.B., Szabo, T.O., Wellington, C.A., Bellgard, M.I.: Yabi: An online research environment for grid, high performance and cloud computing. Source Code for Biology and Medicine 7(1) (2012)Google Scholar
  11. 11.
    Abouelhoda, M., Issa, S.A., Ghanem, M.: Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support. BMC Bioinformatics 13, 77 (2012)CrossRefGoogle Scholar
  12. 12.
    Salem, R., Boussaïd, O., Darmont, J.: Active XML-based Web data integration. Inf. Syst. Front. 15, 371–398 (2013)CrossRefGoogle Scholar
  13. 13.
    Tank, D.M.: Reducing ETL Load Times by a New Data Integration Approach for Real-time Business Intelligence. International Journal of Engineering Innovation and Research 1, 1–5 (2012)Google Scholar
  14. 14.
    Naeem, M.A., Dobbie, G., Webber, G.: An Event-Based Near Real-Time Data Integration Architecture. In: 2008 12th Enterprise Distributed Object Computing Conference Workshops, pp. 401–404 (2008)Google Scholar
  15. 15.
    Mouttham, A., Peyton, L., Eze, B., Saddik, A.E.: Event-Driven Data Integration for Personal Health Monitoring. Journal of Emerging Technologies in Web Intelligence 1(2) (2009), Special Issue: E-health Interoperability (2009) Google Scholar
  16. 16.
    Papazoglou, M., Heuvel, W.-J.: Service oriented architectures: Approaches, technologies and research issues. The VLDB Journal 16, 389–415 (2007)CrossRefGoogle Scholar
  17. 17.
    Kong, J., Jung, J.Y., Park, J.: Event-driven service coordination for business process integration in ubiquitous enterprises. Computers and Industrial Engineering 57, 14–26 (2009)CrossRefGoogle Scholar
  18. 18.
    Niblett, P., Graham, S.: Events and service-oriented architecture: The oasis web services notification specification. IBM Systems Journal 44, 869–886 (2005)CrossRefGoogle Scholar
  19. 19.
    Zhao, Z., Paschke, A.: Event-Driven Scientific Workflow Execution. In: La Rosa, M., Soffer, P. (eds.) BPM Workshops 2012. LNBIP, vol. 132, pp. 390–401. Springer, Heidelberg (2013)CrossRefGoogle Scholar
  20. 20.
    Overbeek, S., Janssen, M., van Bommel, P.: Designing, formalizing, and evaluating a flexible architecture for integrated service delivery: Combining event-driven and service-oriented architectures. Service Oriented Computing and Applications 6, 167–188 (2012)CrossRefGoogle Scholar
  21. 21.
    Frank, J.H., Zeng, L.: On Event-Driven Business Integration. In: 2013 IEEE 10th International Conference on e-Business Engineering (ICEBE), pp. 82–89. IEEE (Year)Google Scholar
  22. 22.
    Fotiou, N., Trossen, D., Polyzos, G.C.: Illustrating a publish-subscribe internet architecture. Telecommunication Systems 51, 233–245 (2012)CrossRefGoogle Scholar
  23. 23.
    Eugster, P.T., Felber, P.A., Guerraoui, R., Kermarrec, A.-M.: The many faces of publish/subscribe. ACM Computing Surveys (CSUR) 35, 114–131 (2003)CrossRefGoogle Scholar
  24. 24.
    Linlin, L., Shizhong, Y.: XPath-Based Filter for Publish/Subscribe in Healthcare Environments. In: 2012 IEEE 12th International Conference on Computer and Information Technology (CIT), pp. 1092–1096 (2012)Google Scholar
  25. 25.
    Yu, H.Q., Zhao, X., Zhen, X., Dong, F., Liu, E., Clapworthy, G.: Healthcare-Event driven semantic knowledge extraction with hybrid data repository. In: 2014 Fourth International Conference on Innovative Computing Technology (INTECH), pp. 13–18. IEEE (2014)Google Scholar
  26. 26.
    Llambias, G., Ruggia, R.: A middleware-based platform for the integration of Bioinformatic services. In: 2014 XL Latin American Computing Conference (CLEI), pp. 1–12. IEEE (2014)Google Scholar
  27. 27.
    Lopes, P., Oliveira, J.L.: An innovative portal for rare genetic diseases research: The semantic Diseasecard. Journal of Biomedical Informatics 46, 1108–1115 (2013)CrossRefGoogle Scholar
  28. 28.
    Lopes, P., Dalgleish, R., Oliveira, J.L.: WAVe: web analysis of the variome. Human Mutation 32, 729–734 (2011)CrossRefGoogle Scholar
  29. 29.
    Lancaster, O., Hastings, R., Dalgleish, R., Atlan, D., Thorisson, G., Free, R., Webb, A., Brookes, A.: Cafe Variome-gene mutation data clearinghouse. Journal of Medical Genetic BMJ, S40–S40 (Year)Google Scholar
  30. 30.
    Fokkema, I.F., Taschner, P.E., Schaafsma, G.C., Celli, J., Laros, J.F., den Dunnen, J.T.: LOVD v. 2.0: The next generation in gene variant databases. Human Mutation 32, 557–563 (2011)CrossRefGoogle Scholar
  31. 31.
    Lopes, P., Oliveira, J.L.: COEUS: “Semantic web in a box” for biomedical applications. Journal of Biomedical Semantics 3, 1–19 (2012)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Pedro Lopes
    • 1
  • José Luís Oliveira
    • 1
  1. 1.Universidade de AveiroAveiroPortugal

Personalised recommendations