SABIO-Reaction Kinetics Database

SABIO-RK (System for the Analysis of

Biochemical Pathways - Reaction
SABIO-RK Database
Kinetics) is a web-accessible database
storing information about biochemical
reactions and their kinetic properties.

SABIO-RK comprises a reaction-

oriented representation of quantitative
information on reaction dynamics based Content
on a given selected publication. This
comprises all available kinetic parameters Description Database for biochemical reactions and
together with their corresponding rate their kinetic properties
equations, as well as kinetic law and Data types Quantitative information on reaction
parameter types and experimental and captured dynamics
environmental conditions under which
Organisms all
the kinetic data were determined.
Additionally, SABIO-RK contains Contact
information about the underlying Research center Heidelberger Institut für Theoretische
biochemical reactions and pathways Studien (http://www.h-its.org/)
including their reaction participants,
cellular location and detailed information Laboratory Scientific Databases and Visualization (ht
about the enzymes catalysing the tp://www.h-its.org/english/research/sdbv/)
reactions.[1][2][3][4][5] Release date 2006
Access
SABIO-RK Database Website http://sabio.h-its.org
Content Web service URL http://sabio.h-
its.org/layouts/content/webservices.gsp
The data stored in SABIO-RK in a Miscellaneous
comprehensive manner is mainly
extracted manually from literature. This License http://sabio.h-
includes reactions, their participants its.org/layouts/content/termscondition.gsp
(substrates, products), modifiers Curation policy Curated database
(inhibitors, activators, cofactors), catalyst
details (e.g. EC enzyme classification, protein complex composition, wild type / mutant information),
kinetic parameters together with corresponding rate equation, biological sources (organism, tissue, cellular
location), environmental conditions (pH, temperature, buffer) and reference details. Data are adapted,
normalized and annotated to controlled vocabularies, ontologies and external data sources including
KEGG, UniProt, ChEBI, PubChem, NCBI, Reactome, BRENDA, MetaCyc, BioModels, and PubMed.
As of October 2021 SABIO-RK contains about 71.000 curated single entries extracted from more than
7.300 publications.
Several tools, databases and workflows in Systems Biology make use of SABIO-RK biochemical reaction
data by integration into their framework including SYCAMORE,[6] MeMo-RK,[7] CellDesigner,[8]
PeroxisomeDB,[9] Taverna workflows or tools like KineticsWizard software for data capture and
analysis.[10] Additionally, SABIO-RK is part of MIRIAM registry, a set of guidelines for the annotation
and curation of computational models[11][12]

SABIO-RK Database Access

The usage of SABIO-RK is free of charge. Commercial users need a license. SABIO-RK offers several
ways for data access:

a browser-based interface
RESTful-based web services for programmatic access

Result data sets can be exported in different formats including SBML, BioPAX/SBPAX, and table format.

References
1. Wittig, U; Rey, M; Weidemann, A; Kania, R; Müller, W (4 January 2018). "SABIO-RK: an
updated resource for manually curated biochemical reaction kinetics" (https://www.ncbi.nlm.
nih.gov/pmc/articles/PMC5753344). Nucleic Acids Research. 46 (D1): D656–D660.
doi:10.1093/nar/gkx1065 (https://doi.org/10.1093%2Fnar%2Fgkx1065). PMC 5753344 (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753344). PMID 29092055 (https://pubmed.ncbi.
nlm.nih.gov/29092055).
2. Wittig, U; Kania, R; Golebiewski, M; Rey, M; Shi, L; Jong, L; Algaa, E; Weidemann, A; Sauer-
Danzwith, H; Mir, S; Krebs, O; Bittkowski, M; Wetsch, E; Rojas, I; Müller, W (January 2012).
"SABIO-RK--database for biochemical reaction kinetics" (https://www.ncbi.nlm.nih.gov/pmc/
articles/PMC3245076). Nucleic Acids Research. 40 (Database issue): D790-6.
doi:10.1093/nar/gkr1046 (https://doi.org/10.1093%2Fnar%2Fgkr1046). PMC 3245076 (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245076). PMID 22102587 (https://pubmed.ncbi.
nlm.nih.gov/22102587).
3. Rojas, I; Golebiewski, M; Kania, R; Krebs, O; Mir, S; Weidemann, A; Wittig, U (2007).
"Storing and annotating of kinetic data". In Silico Biology. 7 (2 Suppl): S37–44.
PMID 17822389 (https://pubmed.ncbi.nlm.nih.gov/17822389).
4. Wittig, Ulrike; Golebiewski, Martin; Kania, Renate; Krebs, Olga; Mir, Saqib; Weidemann,
Andreas; Anstein, Stefanie; Saric, Jasmin; Rojas, Isabel (2006). "SABIO-RK: Integration and
Curation of Reaction Kinetics Data". Data Integration in the Life Sciences. Lecture Notes in
Computer Science. Vol. 4075. pp. 94–103. doi:10.1007/11799511_9 (https://doi.org/10.100
7%2F11799511_9). ISBN 978-3-540-36593-8.
5. Müller W. In: Pfade im Informationsdschungel (http://www.spektrum.de/alias/spektrum-spezia
l-datengetriebene-wissenschaft/pfade-im-informationsdschungel/1129374) Spektrum der
Wissenschaft, Spektrum Spezial: Datengetriebene Wissenschaft, December 2011
6. Weidemann, A.; Richter, S.; Stein, M.; Sahle, S.; Gauges, R.; Gabdoulline, R.; Surovtsova, I.;
Semmelrock, N.; et al. (2008). "SYCAMORE--a systems biology computational analysis and
modeling research environment" (https://doi.org/10.1093%2Fbioinformatics%2Fbtn207).
Bioinformatics. 24 (12): 1463–4. doi:10.1093/bioinformatics/btn207 (https://doi.org/10.1093%
2Fbioinformatics%2Fbtn207). PMID 18463116 (https://pubmed.ncbi.nlm.nih.gov/18463116).
 7. Swainston, Neil; Golebiewski, Martin; Messiha, Hanan L.; Malys, Naglis; Kania, Renate;
Kengne, Sylvestre; Krebs, Olga; Mir, Saqib; et al. (2010). "Enzyme kinetics informatics: From
instrument to browser". FEBS Journal. 277 (18): 3769–79. CiteSeerX 10.1.1.659.3420 (http
s://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.659.3420). doi:10.1111/j.1742-
4658.2010.07778.x (https://doi.org/10.1111%2Fj.1742-4658.2010.07778.x). PMID 20738395
(https://pubmed.ncbi.nlm.nih.gov/20738395). S2CID 20034434 (https://api.semanticscholar.o
rg/CorpusID:20034434).
8. Funahashi, A; Jouraku, A; Matsuoka, Y; Kitano, H (2007). "Integration of CellDesigner and
SABIO-RK". In Silico Biology. 7 (2 Suppl): S81–90. PMID 17822394 (https://pubmed.ncbi.nl
m.nih.gov/17822394).
9. Schluter, A.; Real-Chicharro, A.; Gabaldon, T.; Sanchez-Jimenez, F.; Pujol, A. (2009).
"PeroxisomeDB 2.0: An integrative view of the global peroxisomal metabolome" (https://ww
w.ncbi.nlm.nih.gov/pmc/articles/PMC2808949). Nucleic Acids Research. 38 (Database
issue): D800–5. doi:10.1093/nar/gkp935 (https://doi.org/10.1093%2Fnar%2Fgkp935).
PMC 2808949 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808949). PMID 19892824
(https://pubmed.ncbi.nlm.nih.gov/19892824).
10. Messiha, Hanan L.; Malys, Naglis; Carroll, Kathleen M. (2011). "Towards a Full Quantitative
Description of Yeast Metabolism". Methods in Systems Biology. Methods in Enzymology.
Vol. 500. pp. 215–231. doi:10.1016/B978-0-12-385118-5.00012-8 (https://doi.org/10.1016%2
FB978-0-12-385118-5.00012-8). ISBN 978-0-12-385118-5. PMID 21943900 (https://pubme
d.ncbi.nlm.nih.gov/21943900).
11. Juty, N.; Le Novere, N.; Laibe, C. (2011). "Identifiers.org and MIRIAM Registry: Community
resources to provide persistent identification" (https://www.ncbi.nlm.nih.gov/pmc/articles/PM
C3245029). Nucleic Acids Research. 40 (Database issue): D580–6.
doi:10.1093/nar/gkr1097 (https://doi.org/10.1093%2Fnar%2Fgkr1097). PMC 3245029 (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245029). PMID 22140103 (https://pubmed.ncbi.
nlm.nih.gov/22140103).
12. SABIO-RK as part of MIRIAM Registry (http://www.ebi.ac.uk/miriam/main/mdb?section=brow
se&data=MIR:00000038)

External References
SABIO-RK homepage (http://sabio.h-its.org/)

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