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

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Part of the Lecture Notes in Computer Science book series (LNISA,volume 6799)

Abstract

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.

Keywords

  • 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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References

  1. http://bioserv.rpbs.jussieu.fr/SBMap/

  2. https://wiki.nci.nih.gov/display/caCORE/CORE+Wiki+Home+Page

  3. http://sadi.googlecode.com

  4. Barte, D.: MicroRNAs: target recognition and regulatory functions. Cell 136(2), 215–233 (2009)

    CrossRef  Google Scholar 

  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)

    CrossRef  Google Scholar 

  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)

    CrossRef  Google Scholar 

  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)

    CrossRef  Google Scholar 

  8. Heller, B., Herre, H.: Ontological categories in GOL. Axiomathes 14(1), 57–76 (2004)

    CrossRef  Google Scholar 

  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)

    CrossRef  Google Scholar 

  10. Lacroix, Z., Aziz, M.: Resource descriptions, ontology, and resource discovery. IJMSO 5(3), 194–207 (2010)

    CrossRef  Google Scholar 

  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. 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)

    CrossRef  Google Scholar 

  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)

    CrossRef  Google Scholar 

  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. 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. Vandervalk, B., McCarthy, E., Wilkinson, M.: Moby and Moby 2: creatures of the deep (web). Briefings in bioinformatics 10(2), 114 (2009)

    CrossRef  Google Scholar 

  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)

    CrossRef  Google Scholar 

  18. Wilkinson, M., Links, M.: BioMOBY: an open source biological web services proposal. Briefings in bioinformatics 3(4), 331 (2002)

    CrossRef  Google Scholar 

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Bazzi, R.A., Kiefer, J.M., Lacroix, Z. (2012). A User-Centric Classification of Tools for Biological Resource Discovery and Integration on the Web. In: Lacroix, Z., Vidal, M.E. (eds) Resource Discovery. RED 2010. Lecture Notes in Computer Science, vol 6799. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-27392-6_6

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  • DOI: https://doi.org/10.1007/978-3-642-27392-6_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-27391-9

  • Online ISBN: 978-3-642-27392-6

  • eBook Packages: Computer ScienceComputer Science (R0)