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Enabling Annotation Provenance in Bioinformatics Workflow Applications

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Part of the Lecture Notes in Computer Science book series (LNBI,volume 6268)

Abstract

Nowadays, the resulting data of each step of genomic annotation processes are typically used for annotation provenance. However, recent initiatives in the direction of capturing annotation provenance data do not support the Bioinformatics developer on building their own provenance enabled applications. This work proposes the ArCaP architecture, which aims at supporting the development of provenance enabled applications and at facilitating the access to annotation provenance data. Although the focus is on Bioinformatics applications, this approach is useful to other scientific domains.

Keywords

  • Data provenance
  • Annotation Provenance
  • Scientific Workflows

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References

  1. Altintas, I., Barney, O., Jaeger-Frank, E.: Provenance collection support in the kepler scientific workflow system. Journal Provenance and Annotation of Data (2008)

    Google Scholar 

  2. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Wheeler, D.L.: GenBank. Nucleic Acids Research 36, D25–D30 (2008) doi:10.1093/nar/gkm929

    CrossRef  Google Scholar 

  3. Buneman, P., Chapman, A., Cheney, J.: Provenance management in curated databases. In: Proc. of the 2006 ACM SIGMOD Int. Conf. on Management of Data, SIGMOD ’06, Chicago, IL, USA, June 27-29, pp. 539–550. ACM, New York (2006)

    CrossRef  Google Scholar 

  4. Cavalcanti, M.C., Mattoso, M.L., Campos, M.L.M.: Scientific resources management: Towards an in Silico Laboratory. Tech. Rep., UFRJ (2003)

    Google Scholar 

  5. Baumgartner Jr., W.A., Cohen, K.B., Fox, L.M., Acquaah-Mensah, G., Hunter, L.: Manual curation is not sufficient for annotation of genomic databases. Bioinformatics 23(13), 41–48 (2007)

    CrossRef  Google Scholar 

  6. Lord, P., Macdonald, A., Lyon, L., Giaretta, D.: From Data Deluge to Data Curation. The Digital Archiving Consultancy Limited and the Digital Curation Centre (2004)

    Google Scholar 

  7. Menezes, J.G.M.: Gerência distribuida de dados em workflows de bioinformática. Master Thesis, Military Institute of Engineering - IME (2008)

    Google Scholar 

  8. Oswaldo Cruz Institute/Fiocruz, http://www.fiocruz.br

  9. Scheidegger, C., Koop, D., Santos, E., Vo, H., Callahan, S., Freire, J., Silva, C.: Tackling the provenance challenge one layer at a time. Concurrency and Computation: Practice and Experience (2007)

    Google Scholar 

  10. Simmhan, Y., Plale, B., Gannon, D.: Karma2: Provenance management for data driven workflows. Int. Journal of Web Services Research 5(1) (2008)

    Google Scholar 

  11. Moreau, L., Freire, J., Futrelle, J., Mcgrath, R., Myers, J., Paulson, P.: The open provenance model. Technical report, University of Southampton (2007)

    Google Scholar 

  12. Guimarães, M.P.: Uma abordagem para capturar a proveniência de dados na área de Bioinformática. Master Thesis, Military Institute of Engineering - IME (2009)

    Google Scholar 

  13. System for Integrate Genomic Resources and Analysis, stingray.biowebdb.org

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Guimarães, M.P., Cavalcanti, M.C. (2010). Enabling Annotation Provenance in Bioinformatics Workflow Applications. In: Ferreira, C.E., Miyano, S., Stadler, P.F. (eds) Advances in Bioinformatics and Computational Biology. BSB 2010. Lecture Notes in Computer Science(), vol 6268. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15060-9_7

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  • DOI: https://doi.org/10.1007/978-3-642-15060-9_7

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-15059-3

  • Online ISBN: 978-3-642-15060-9

  • eBook Packages: Computer ScienceComputer Science (R0)