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An Ontology and a REST API for Sequence Based Microbial Typing Data

  • João Almeida
  • João Tiple
  • Mário Ramirez
  • José Melo-Cristino
  • Cátia Vaz
  • Alexandre P. Francisco
  • João A. Carriço
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6620)

Abstract

In the Microbial typing field, the need to have a common understanding of the concepts described and the ability to share results within the community is an increasingly important requisite for the continued development of portable and accurate sequence-based typing methods. These methods are used for bacterial strain identification and are fundamental tools in Clinical Microbiology and Bacterial Population Genetics studies. In this article we propose an ontology designed for the microbial typing field, focusing on the widely used Multi Locus Sequence Typing methodology, and a RESTful API for accessing information systems based on the proposed ontology. This constitutes an important first step to accurately describe, analyze, curate, and manage information for microbial typing methodologies based on sequence based typing methodologies, and allows for the future integration with data analysis Web services.

Keywords

ontology knowledge representation data as a service microbial typing methods 

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References

  1. 1.
    Aguiar, S., Serrano, I., Pinto, F., Melo-Cristino, J., Ramirez, M.: Changes in Streptococcus pneumoniae serotypes causing invasive disease with non-universal vaccination coverage of the seven-valent conjugate vaccine. Clinical Microbiology and Infection 14(9), 835–843 (2008)CrossRefGoogle Scholar
  2. 2.
    Fielding, R.: Architectural styles and the design of network-based software architectures. Ph.D. thesis, Citeseer (2000)Google Scholar
  3. 3.
    Harris, S., Feil, E., Holden, M., Quail, M., Nickerson, E., Chantratita, N., Gardete, S., Tavares, A., Day, N., Lindsay, J., et al.: Evolution of MRSA during hospital transmission and intercontinental spread. Science 327(5964), 469 (2010)CrossRefGoogle Scholar
  4. 4.
    MacLean, D., Jones, J., Studholme, D.: Application of’next-generation’sequencing technologies to microbial genetics. Nature Reviews Microbiology 7(4), 287–296 (2009)Google Scholar
  5. 5.
    Mwangi, M., Wu, S., Zhou, Y., Sieradzki, K., De Lencastre, H., Richardson, P., Bruce, D., Rubin, E., Myers, E., Siggia, E., et al.: Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing. Proceedings of the National Academy of Sciences 104(22), 9451 (2007)CrossRefGoogle Scholar
  6. 6.
    Spratt, B.: Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet. Current Opinion in Microbiology 2(3), 312–316 (1999)MathSciNetCrossRefGoogle Scholar
  7. 7.
    Van Belkum, A., Struelens, M., De Visser, A., Verbrugh, H., Tibayrenc, M.: Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology. Clinical Microbiology Reviews 14(3), 547 (2001)CrossRefGoogle Scholar
  8. 8.
    Institut Pasteur MLST Databases. Pasteur Institute, http://www.pasteur.fr/mlst/
  9. 9.
    Jena A Semantic Web Framework for Java. HP and Others, http://jena.sourceforge.net/
  10. 10.
    MLST: Multi Locus Sequence Typing. Imperial College of London, http://www.mlst.net
  11. 11.
    The Protégé Ontology Editor and Knowledge Acquisition System. Stanford Center for Biomedical Informatics Research, http://protege.stanford.edu
  12. 12.
    PubMLST. University of Oxford (UK), http://pubmlst.org/
  13. 13.
    Ridom SpaServer. Ridom bioinformatics, http://www.spaserver.ridom.de/
  14. 14.
    Streptococcus pyogenes emm sequence database. CDC, http://www.cdc.gov/ncidod/biotech/strep/M-ProteinGene_typing.htm

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • João Almeida
    • 1
  • João Tiple
    • 1
  • Mário Ramirez
    • 2
  • José Melo-Cristino
    • 2
  • Cátia Vaz
    • 1
    • 3
  • Alexandre P. Francisco
    • 3
    • 4
  • João A. Carriço
    • 2
  1. 1.DEETC, ISELPoly Inst. of LisbonPortugal
  2. 2.IM / IMM, FMUniv. of LisbonPortugal
  3. 3.INESC-ID LisbonPortugal
  4. 4.CSE Dept., ISTTech. Univ. of LisbonPortugal

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