Chapter

Data Integration in the Life Sciences

Volume 4075 of the series Lecture Notes in Computer Science pp 94-103

SABIO-RK: Integration and Curation of Reaction Kinetics Data

  • Ulrike WittigAffiliated withCarnegie Mellon UniversityScientific Databases and Visualization Group, EML Research gGmbH
  • , Martin GolebiewskiAffiliated withCarnegie Mellon UniversityScientific Databases and Visualization Group, EML Research gGmbH
  • , Renate KaniaAffiliated withCarnegie Mellon UniversityScientific Databases and Visualization Group, EML Research gGmbH
  • , Olga KrebsAffiliated withCarnegie Mellon UniversityScientific Databases and Visualization Group, EML Research gGmbH
  • , Saqib MirAffiliated withCarnegie Mellon UniversityScientific Databases and Visualization Group, EML Research gGmbH
  • , Andreas WeidemannAffiliated withCarnegie Mellon UniversityScientific Databases and Visualization Group, EML Research gGmbH
  • , Stefanie AnsteinAffiliated withCarnegie Mellon UniversityScientific Databases and Visualization Group, EML Research gGmbH
  • , Jasmin SaricAffiliated withCarnegie Mellon UniversityScientific Databases and Visualization Group, EML Research gGmbH
  • , Isabel RojasAffiliated withCarnegie Mellon UniversityScientific Databases and Visualization Group, EML Research gGmbH

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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.