SABIO-RK: Integration and Curation of Reaction Kinetics Data


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.


Projects: F3: Kinetic data handling

Data Integration in the Life Sciences
Lecture Notes in Computer Science 4075 : 94

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

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[Ulrike Wittig] [Martin Golebiewski] [Andreas Weidemann] [Renate Kania]

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Views: 2238
  • Created: 26th Jul 2011 at 18:33
  • Last updated: 24th Oct 2013 at 16:24

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