Welcome to the SABIO-Reaction Kinetics Database
(last software update 2012/02/07 09:43)

The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modellers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. Information about reactions and their kinetics can be exported in SBML (Systems Biology Mark-Up Language ) format.

Please use the following reference to cite SABIO-RK:
SABIO-RK: Integration and Curation of Reaction Kinetics Data Wittig U., Golebiewski, M., Kania, R., Krebs, O., Mir, S., Weidemann, A., Anstein, S., Saric, J. and Rojas, I.. In proceedings of the 3rd International workshop on Data Integration in the Life Sciences 2006 (DILS'06). Hinxton, UK. Lecture Notes in Bioinformatics, 4075: 94-103(2006).
Abstract

There are two main sources for the data contained in SABIO. Most of the reactions, their association with pathways and their enzymatic classification, is extracted from the KEGG (KEGG: Kyoto Encyclopedia of Genes and Genomes) database. The other main source of data are publications. The reaction kinetics data are obtained by manual extraction from literature sources and curated.

1. Allows the querying for reactions:
   • within pathway(s)
   • having certain reactant(s)
   • classified with EC Number
   • reported to occur in organism(s) -- from curated data
   • reported to occur in tissue(s)/cell type(s) -- from curated data
   • reported to occur in cellular location -- from curated data
   • reported to occur at a certain temperature/pH -- from curated data
   • reported about in certain publication -- giving PubMed ID
2. Link to Swissprot and PubMed
3. Generation of SBML format file, containing information about the reactions, their kinetic laws (if existing) and parameter definition and values.
   PLEASE NOTE: the SBML file generated needs to be edited before it can be used by most modelling tools supporting SBML, given that the system will create as many unit definition as defined for the parameters. Thus the user needs to preform the unit convertion in order to have all parameter values defined using the same basic units. We plan to include information about in vivo compound concentrations in the near future, which can then included into the SBML file. Currently all compound concentration will be set to 1.