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.
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: an updated resource for manually curated biochemical reaction kinetics
Ulrike Wittig, Maja Rey, Andreas Weidemann, Renate Kania, Wolfgang Müller
Nucleic Acids Research, Database issue (2018) https://doi.org/10.1093/nar/gkx1065
You can find more information on SABIO-RK in the following publications:
Improved insights into the SABIO-RK database via visualization
Dorotea Dudaš, Ulrike Wittig, Maja Rey, Andreas Weidemann, Wolfgang Müller
Database, Volume 2023, baad011 (2023) https://doi.org/10.1093/database/baad011
Challenges for an enzymatic reaction kinetics database
Ulrike Wittig, Maja Rey, Renate Kania, Meik Bittkowski, Lei Shi, Martin Golebiewski, Andreas Weidemann, Wolfgang Müller, and Isabel Rojas
FEBS Journal, 281(2):572-582 (2014)
http://onlinelibrary.wiley.com/doi/10.1111/febs.12562/abstract
Data extraction for the reaction kinetics database SABIO-RK
Ulrike Wittig, Renate Kania, Meik Bittkowski, Elina Wetsch, Lei Shi, Lenneke Jong, Martin Golebiewski, Maja Rey, Andreas Weidemann, Isabel Rojas, Wolfgang Müller
Perspectives in Science 1, 33–40 (2014)
http://www.sciencedirect.com/science/article/pii/S2213020914000056
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, 40 (Database issue):D790-6 (2012)
http://nar.oxfordjournals.org/content/40/D1/D790
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
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, (ISSN 1613-4516), 4(1) (2007)
http://biecoll.ub.uni-bielefeld.de/volltexte/2007/230
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
