About

SABIO-RK is a curated database containing structured information about biochemical reactions and their corresponding kinetics. It describes participants and modifiers of the reactions, as well as measured kinetic data (including kinetic rate equations) embedded in their experimental and environmental context. The system offers standardized data for metabolic and newly also signaling reactions by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. It enables the access to kinetic data for experimentalists and modellers. Thereby, SABIO-RK facilitates the exchange of the data between experimentalists and modellers, supporting the setup of quantitative computer models.

a picture about Sabo-Rk's Workflow

The data in SABIO-RK is either manually extracted from pub-
lished literature or directly submitted by experimenters. It is curated by experts and supplemented with additional information from other data-
bases and biological ontologies. The database can be accessed either manually via a web-based search interface or via web services that allow direct automated access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup
Language) complying with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. Confidential data, such as directly submitted pre-publication data, can be hidden for public access by defining the sharing rights for named users.



Publications

Please use the following reference to cite SABIO-RK:

SABIO-RK - database for biochemical reaction kinetics

Ulrike Wittig; Renate Kania; Martin Golebiewski; Maja Rey; Lei Shi; Lenneke Jong;
Enkhjargal Algaa; Andreas Weidemann; Heidrun Sauer-Danzwith; Saqib Mir; Olga Krebs; Meik Bittkowski; Elina Wetsch; Isabel Rojas; Wolfgang Müller
Nucleic Acids Research 2012;40(Database issue):D790-6
http://nar.oxfordjournals.org/content/40/D1/D790


You can find more information on SABIO-RK in the following publications:

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
Lecture Notes in Bioinformatics, 4075: 94-103 (2006)
http://dx.doi.org/10.1007/11799511_9

Storing and annotating of kinetic data

Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann,
Ulrike Wittig
In Silico Biology, 7(2 Suppl):S37-44 (2007)
PMID: 17822389
http://www.bioinfo.de/isb/2007/07/S1/05/

SABIO-RK: a database for biochemical reactions and their kinetics

Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann,
Ulrike Wittig
BMC Systems Biology, 1(Suppl 1):S6 (2007)
http://www.biomedcentral.com/1752-0509/1/S1/S6

Integration of SABIO-RK in workbenches for kinetic model design

Martin Golebiewski, Saqib Mir, Renate Kania, Olga Krebs, Andreas Weidemann, Ulrike Wittig,
Isabel Rojas
BMC Systems Biology, 1(Suppl 1):P4 (2007)
http://www.biomedcentral.com/1752-0509/1/S1/P4

SABIO-RK: A data warehouse for biochemical reactions and their kinetics

Olga Krebs, Martin Golebiewski, Renate Kania, Saqib Mir, Jasmin Saric, Andreas Weidemann,
Ulrike Wittig, Isabel Rojas
Journal of Integrative Bioinformatics,
http://biecoll.ub.uni-bielefeld.de/volltexte/2007/230

Enzyme kinetics informatics: from instrument to browser

Neil Swainston, Martin Golebiewski, Hanan L. Messiha, Naglis Malys, Renate Kania, Sylvestre Kengne,
Olga Krebs, Saqib Mir, Heidrun Sauer-Danzwith, Kieran Smallbone, Andreas Weidemann, Ulrike Wittig, Douglas B. Kell, Pedro Mendes, Wolfgang Müller, Norman W. Paton, Isabel Rojas
FEBS Journal, Vol. 277 (Issue 18): 3769-3779 (2010)
http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2010.07778.x/abstract