A User-Centric Classification of Tools for Biological Resource Discovery and Integration on the Web

  • Rida A. Bazzi
  • Jeffrey M. Kiefer
  • Zoé Lacroix
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6799)


The need to use resource discovery and composition tools to assist in the development of scientific workflows is well established. While systems have been developed to guide scientists in the design and implementation of their protocols into executable workflows, these systems differ significantly in the way they support the various steps of resource discovery. This paper proposes a classification of resource exploration and discovery tools according to five main categories: content, graphical interface, maintenance, optimization, and query. The paper overviews six resource discovery approaches and evaluates them according to the proposed classification. An example of how the metrics can be used in the selection of an appropriate tool for given requirements is presented.


Graphical Interface Service Discovery Domain Ontology Resource Discovery Graphical View 
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.
  2. 2.
  3. 3.
  4. 4.
    Barte, D.: MicroRNAs: target recognition and regulatory functions. Cell 136(2), 215–233 (2009)CrossRefGoogle Scholar
  5. 5.
    Boulakia, S.C., Davidson, S.B., Froidevaux, C., Lacroix, Z., Vidal, M.-E.: Path-based systems to guide scientists in the maze of biological data sources. J. Bioinformatics and Computational Biology 4(5), 1069–1096 (2006)CrossRefGoogle Scholar
  6. 6.
    Dinov, I., Rubin, D., Lorensen, W., Dugan, J., Ma, J., Murphy, S., Kirschner, B., Bug, W., Sherman, M., Floratos, A., Kennedy, D., Jagadish, H., Schmidt, J., Athey, B., Califano, A., Musen, M., Altman, R., Kikinis, R., Kohane, I., Delp, S., Parker, D., Toga, A.: iTools: a framework for classification, categorization and integration of computational biology resources. PloS One 3(5), e2265 (2008)CrossRefGoogle Scholar
  7. 7.
    Duchateau, F., Coletta, R., Bellahsene, Z., Miller, R.J.: Yam: a schema matcher factory. In: Cheung, D.W.-L., Song, I.-Y., Chu, W.W., Hu, X., Lin, J.J. (eds.) CIKM, pp. 2079–2080. ACM, New York (2009)CrossRefGoogle Scholar
  8. 8.
    Heller, B., Herre, H.: Ontological categories in GOL. Axiomathes 14(1), 57–76 (2004)CrossRefGoogle Scholar
  9. 9.
    Kinsy, M., Lacroix, Z., Legendre, C., Wlodarczyk, P., Ayadi, N.Y.: ProtocolDB: Storing scientific protocols with a domain ontology. In: Weske, M., Hacid, M.-S., Godart, C. (eds.) WISE Workshops 2007. LNCS, vol. 4832, pp. 17–28. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  10. 10.
    Lacroix, Z., Aziz, M.: Resource descriptions, ontology, and resource discovery. IJMSO 5(3), 194–207 (2010)CrossRefGoogle Scholar
  11. 11.
    Lacroix, Z., Legendre, C., Tuzmen, S.: Reasoning on scientific workflows. In: SERVICES I, pp. 306–313. IEEE Computer Society, Los Alamitos (2009)Google Scholar
  12. 12.
    Lacroix, Z., Parekh, K., Vidal, M.-E., Cardenas, M., Marquez, N.: BioNavigation: Selecting optimum paths through biological resources to evaluate ontological navigational queries. In: Ludäscher, B., Raschid, L. (eds.) DILS 2005. LNCS (LNBI), vol. 3615, pp. 275–283. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  13. 13.
    Lacroix, Z., Vidal, M.-E., Legendre, C.: Customized and optimized service selection with protocolDB. In: Hameurlain, A., Tjoa, A.M. (eds.) Globe 2009. LNCS, vol. 5697, pp. 112–123. Springer, Heidelberg (2009)CrossRefGoogle Scholar
  14. 14.
    Strauser, E., Naveau, M., Ménager, H., Maupetit, J., Lacroix, Z., Tuffery, P.: Semantic Map for Structural Bioinformatics: enhanced service discovery based on high level concept ontology. In: Lacroix, Z., Vidal, M.E. (eds.) RED 2010. LNCS, vol. 6799, pp. 77–93. Springer, Heidelberg (2010)Google Scholar
  15. 15.
    Tufféry, P., Lacroix, Z., Ménager, H.: Semantic map of services for structural bioinformatics. In: SSDBM, pp. 217–224. IEEE Computer Society, Los Alamitos (2006)Google Scholar
  16. 16.
    Vandervalk, B., McCarthy, E., Wilkinson, M.: Moby and Moby 2: creatures of the deep (web). Briefings in bioinformatics 10(2), 114 (2009)CrossRefGoogle Scholar
  17. 17.
    Vandervalk, B.P., McCarthy, E.L., Wilkinson, M.D.: SHARE: A semantic web query engine for bioinformatics. In: Gómez-Pérez, A., Yu, Y., Ding, Y. (eds.) ASWC 2009. LNCS, vol. 5926, pp. 367–369. Springer, Heidelberg (2009)CrossRefGoogle Scholar
  18. 18.
    Wilkinson, M., Links, M.: BioMOBY: an open source biological web services proposal. Briefings in bioinformatics 3(4), 331 (2002)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Rida A. Bazzi
    • 1
  • Jeffrey M. Kiefer
    • 2
  • Zoé Lacroix
    • 1
    • 2
  1. 1.Arizona State UniversityTempeUSA
  2. 2.Translational Genomics Research InstitutePhoenixUSA

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