A Dataflow Platform for In-silico Experiments Based on Linked Data

  • Paolo Bottoni
  • Miguel Ceriani
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8381)


A big part of the work carried out by scientists nowadays involves data manipulation: access and integration of different local and online datasets, filtering for relevant information, aggregating and visualising the data to look for or defend hypotheses. The Linked Data Initiative is pushing dataset maintainers to publish data in a highly reusable way through a set of open standards, such as RDF and SPARQL. The adoption of these technologies in the scientific community is still marginal, partly for the limits of the available tools for consuming and manipulating data. We present a concrete pipeline language and a working prototype (including a visual editor and a pipeline engine) by which users can build and share applications consuming and visualising linked data.


Resource Description Framework Network Graph SPARQL Query Scalable Vector Graphic Resource Description Framework Data 
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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  1. 1.
    Bray, T., Paoli, J., Sperberg-McQueen, C.M., Maler, E., Yergeau, F., Cowan, J.: Extensible Markup Language (XML) 1.1 (Second Edition). W3C Recommendation 16 August 2006, edited in place 29 September 2006Google Scholar
  2. 2.
    Klyne, G., Carroll, J.J., McBride, B.: Resource Description Framework (RDF): Concepts and Abstract Syntax. W3C Recommendation (February 10, 2004)Google Scholar
  3. 3.
    Berners-Lee, T., Hendler, J., Lassila, O.: The semantic web. Scientific American 284(5), 34–43 (2001)CrossRefGoogle Scholar
  4. 4.
    Harris, S., et al.: SPARQL 1.1 Query Language. W3C Recommendation (March 21, 2013)Google Scholar
  5. 5.
    Cyganiak, R., Wood, D., Lanthaler, M.: RDF 1.1 Concepts and Abstract Syntax. W3C Candidate Recommendation (November 5, 2013)Google Scholar
  6. 6.
    Mallea, A., Arenas, M., Hogan, A., Polleres, A.: On Blank Nodes. In: Aroyo, L., Welty, C., Alani, H., Taylor, J., Bernstein, A., Kagal, L., Noy, N., Blomqvist, E. (eds.) ISWC 2011, Part I. LNCS, vol. 7031, pp. 421–437. Springer, Heidelberg (2011)CrossRefGoogle Scholar
  7. 7.
    Schenk, S., Gearon, P., et al.: SPARQL 1.1 Update. W3C Recommendation (March 21, 2013)Google Scholar
  8. 8.
    Prud’hommeaux, E., Seaborne, A.: SPARQL Query Language for RDF. W3C Recommendation (January 15, 2008)Google Scholar
  9. 9.
    Andersson, O., Armstrong, P., Axelsson, H., Berjon, R., Bzaire, B., et al.: Scalable Vector Graphics (SVG) 1.1 Specification. W3C Recommendation (January 14, 2003)Google Scholar
  10. 10.
    Pixley, T.: Document Object Model (DOM) Level 2 Events Specification. W3C Recommendation (November 13, 2000)Google Scholar
  11. 11.
    Kacmarcik, G., Leithead, T., Rossi, J., Schepers, D., Hhrmann, B., Le Hgaret, P., Pixley, T.: Document Object Model (DOM) Level 3 Events Specification. W3C Recommendation (November 13, 2000)Google Scholar
  12. 12.
    Google: Google charts (2010)Google Scholar
  13. 13.
    Belmonte, N.G.: Javascript infovis toolkit (2011)Google Scholar
  14. 14.
    Bostock, M., Ogievetsky, V., Heer, J.: D3: Data-driven documents. IEEE Trans. Visualization & Comp. Graphics, Proc. InfoVis (2011)Google Scholar
  15. 15.
    Smits, S.A., Ouverney, C.C.: jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web. PloS one 5(8), e12267 (2010)Google Scholar
  16. 16.
    Magkanaraki, A., Tannen, V., Christophides, V., Plexousakis, D.: Viewing the Semantic Web through RVL Lenses. In: Fensel, D., Sycara, K., Mylopoulos, J. (eds.) ISWC 2003. LNCS, vol. 2870, pp. 96–112. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  17. 17.
    Karvounarakis, G., Magkanaraki, A., Alexaki, S., Christophides, V., Plexousakis, D., Scholl, M., Tolle, K.: Rql: A functional query language for rdf. In: Gray, P.D., Kerschberg, L., King, P.H., Poulovassilis, A. (eds.) The Functional Approach to Data Management, pp. 435–465. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  18. 18.
    Shaw, M., Detwiler, L.T., Noy, N., Brinkley, J., Suciu, D.: vSPARQL: A view definition language for the semantic web. Journal of Biomedical Informatics 44(1), 102–117 (2011); Ontologies for Clinical and Translational ResearchGoogle Scholar
  19. 19.
    Schenk, S., Staab, S.: Networked graphs: a declarative mechanism for SPARQL rules, SPARQL views and RDF data integration on the web. In: Proc. WWW 2008, pp. 585–594. ACM (2008)Google Scholar
  20. 20.
    Chandra, A.K., Harel, D.: Horn clause queries and generalizations. The Journal of Logic Programming 2(1), 1–15 (1985)CrossRefMathSciNetzbMATHGoogle Scholar
  21. 21.
    ISO-ANSI: Database language sql-part2: Sql/foundation. Technical Report 9075-2 edition, ANSI, ISO 9075-2 edition (1999)Google Scholar
  22. 22.
    Van Gelder, A., Ross, K.A., Schlipf, J.S.: The well-founded semantics for general logic programs. Journal of the ACM (JACM) 38(3), 619–649 (1991)CrossRefGoogle Scholar
  23. 23.
    Van Gelder, A.: The alternating fixpoint of logic programs with negation. Journal of Computer and System Sciences 47(1), 185–221 (1993)CrossRefMathSciNetzbMATHGoogle Scholar
  24. 24.
    Le-Phuoc, D., Polleres, A., Hauswirth, M., Tummarello, G., Morbidoni, C.: Rapid prototyping of semantic mash-ups through semantic web pipes. In: Proc. WWW 2009, pp. 581–590. ACM (2009)Google Scholar
  25. 25.
    Knublauch, H., et al.: SPARQLMotion Specifications (2010),
  26. 26.
    Fürber, C., Hepp, M.: Using SPARQL and SPIN for data quality management on the semantic web. In: Abramowicz, W., Tolksdorf, R. (eds.) BIS 2010. LNBIP, vol. 47, pp. 35–46. Springer, Heidelberg (2010)CrossRefGoogle Scholar
  27. 27.
    Graves, A.: Creation of visualizations based on linked data. In: Proceedings of the 3rd International Conference on Web Intelligence, Mining and Semantics, vol. 41, ACM (2013)Google Scholar
  28. 28.
    Battle, S., Wood, D., Leigh, J., Ruth, L.: The Callimachus Project: RDFa as a Web Template Language. In: COLD (2012)Google Scholar
  29. 29.
    Shinavier, J.: Functional programs as linked data. In: 3rd Workshop on Scripting for the Semantic Web (2007)Google Scholar
  30. 30.
    Braatz, B., Brandt, C.: How to Modify on the semantic web? In: Daniel, F., Facca, F.M. (eds.) ICWE 2010. LNCS, vol. 6385, pp. 187–198. Springer, Heidelberg (2010)CrossRefGoogle Scholar
  31. 31.
    Apparao, V., Byrne, S., Champion, M., Isaacs, S., et al.: Document Object Model (DOM) Level 1 Specification - Version 1.0. W3C Recommendation (October 1, 1998)Google Scholar
  32. 32.
    Ogbuji, C.: Sparql 1.1 Graph Store HTTP Protocol. W3C Recommendation (March 21, 2013)Google Scholar
  33. 33.
    McBride, B.: Jena: a semantic Web toolkit. IEEE Internet Computing 6(6), 55–59 (2002)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Paolo Bottoni
    • 1
  • Miguel Ceriani
    • 1
  1. 1.SapienzaUniversity of RomeItaly

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