SABIO-RK: Integration and Curation of Reaction Kinetics Data

  • Ulrike Wittig
  • Martin Golebiewski
  • Renate Kania
  • Olga Krebs
  • Saqib Mir
  • Andreas Weidemann
  • Stefanie Anstein
  • Jasmin Saric
  • Isabel Rojas
Conference paper

DOI: 10.1007/11799511_9

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4075)
Cite this paper as:
Wittig U. et al. (2006) SABIO-RK: Integration and Curation of Reaction Kinetics Data. In: Leser U., Naumann F., Eckman B. (eds) Data Integration in the Life Sciences. DILS 2006. Lecture Notes in Computer Science, vol 4075. Springer, Berlin, Heidelberg

Abstract

Simulating networks of biochemical reactions require reliable kinetic data. In order to facilitate the access to such kinetic data we have developed SABIO-RK, a curated database with information about biochemical reactions and their kinetic properties. The data are manually extracted from literature and verified by curators, concerning standards, formats and controlled vocabularies. This process is supported by tools in a semi-automatic manner. SABIO-RK contains and merges information about reactions such as reactants and modifiers, organism, tissue and cellular location, as well as the kinetic properties of the reactions. The type of the kinetic mechanism, modes of inhibition or activation, and corresponding rate equations are presented together with their parameters and measured values, specifying the experimental conditions under which these were determined. Links to other databases enable the user to gather further information and to refer to the original publication. Information about reactions and their kinetic data can be exported to an SBML file, allowing users to employ the information as the basis for their simulation models.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Ulrike Wittig
    • 1
  • Martin Golebiewski
    • 1
  • Renate Kania
    • 1
  • Olga Krebs
    • 1
  • Saqib Mir
    • 1
  • Andreas Weidemann
    • 1
  • Stefanie Anstein
    • 1
  • Jasmin Saric
    • 1
  • Isabel Rojas
    • 1
  1. 1.Scientific Databases and Visualization GroupEML Research gGmbHHeidelbergGermany

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