SABIO-Reaction Kinetics Database
{{infobox biodatabase
|title = SABIO-RK Database
|logo = SABIO-RK.jpg
|description = Database for biochemical reactions and their kinetic properties
|scope = Quantitative information on reaction dynamics
|organism = all
|center = [http://www.h-its.org/ Heidelberger Institut für Theoretische Studien]
|laboratory = [http://www.h-its.org/english/research/sdbv/ Scientific Databases and Visualization]
|author =
|pmid =
|released = 2006
|standard =
|format =
|url = http://sabio.h-its.org
|download =
|webservice = http://sabio.h-its.org/layouts/content/webservices.gsp
|sql =
|sparql =
|webapp =
|standalone =
|license = http://sabio.h-its.org/layouts/content/termscondition.gsp
|versioning =
|frequency =
|curation = Curated database
}}
SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction 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 on a given selected publication.
This comprises all available kinetic parameters together with their corresponding rate equations,
as well as kinetic law and parameter types and experimental and environmental conditions under which the kinetic data were determined.
Additionally, SABIO-RK contains information about the underlying biochemical reactions and pathways including their reaction participants,
cellular location and detailed information about the enzymes catalysing the reactions.{{cite journal |last1=Wittig |first1=U |last2=Rey |first2=M |last3=Weidemann |first3=A |last4=Kania |first4=R |last5=Müller |first5=W |title=SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. |journal=Nucleic Acids Research |date=4 January 2018 |volume=46 |issue=D1 |pages=D656–D660 |doi=10.1093/nar/gkx1065 |pmid=29092055|pmc=5753344 }}{{cite journal |last1=Wittig |first1=U |last2=Kania |first2=R |last3=Golebiewski |first3=M |last4=Rey |first4=M |last5=Shi |first5=L |last6=Jong |first6=L |last7=Algaa |first7=E |last8=Weidemann |first8=A |last9=Sauer-Danzwith |first9=H |last10=Mir |first10=S |last11=Krebs |first11=O |last12=Bittkowski |first12=M |last13=Wetsch |first13=E |last14=Rojas |first14=I |last15=Müller |first15=W |title=SABIO-RK--database for biochemical reaction kinetics. |journal=Nucleic Acids Research |date=January 2012 |volume=40 |issue=Database issue |pages=D790-6 |doi=10.1093/nar/gkr1046 |pmid=22102587|pmc=3245076 }}{{cite journal |pmid=17822389 |year=2007 |last1=Rojas |first1=I |last2=Golebiewski |first2=M |last3=Kania |first3=R |last4=Krebs |first4=O |last5=Mir |first5=S |last6=Weidemann |first6=A |last7=Wittig |first7=U |title=Storing and annotating of kinetic data |volume=7 |issue=2 Suppl |pages=S37–44 |journal=In Silico Biology}}{{cite book |doi = 10.1007/11799511_9|chapter = SABIO-RK: Integration and Curation of Reaction Kinetics Data|title = Data Integration in the Life Sciences|series = Lecture Notes in Computer Science|year = 2006|last1 = Wittig|first1 = Ulrike|last2 = Golebiewski|first2 = Martin|last3 = Kania|first3 = Renate|last4 = Krebs|first4 = Olga|last5 = Mir|first5 = Saqib|last6 = Weidemann|first6 = Andreas|last7 = Anstein|first7 = Stefanie|last8 = Saric|first8 = Jasmin|last9 = Rojas|first9 = Isabel|volume = 4075|pages = 94–103|isbn = 978-3-540-36593-8}}Müller W. In:
[http://www.spektrum.de/alias/spektrum-spezial-datengetriebene-wissenschaft/pfade-im-informationsdschungel/1129374 Pfade im Informationsdschungel] Spektrum der Wissenschaft, Spektrum Spezial: Datengetriebene Wissenschaft, December 2011
SABIO-RK Database Content
The data stored in SABIO-RK in a comprehensive manner is mainly extracted manually from literature. This includes reactions, their participants (substrates, products), modifiers (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
Taverna workflows
or tools like KineticsWizard software for data capture and analysis.{{cite book |doi=10.1016/B978-0-12-385118-5.00012-8 |pmid=21943900 |chapter=Towards a Full Quantitative Description of Yeast Metabolism |title=Methods in Systems Biology |series=Methods in Enzymology |year=2011 |last1=Messiha |first1=Hanan L. |last2=Malys |first2=Naglis |last3=Carroll |first3=Kathleen M. |isbn=978-0-12-385118-5 |volume=500 |pages=215–231}}
Additionally, SABIO-RK is part of MIRIAM registry, a set of guidelines for the annotation and curation of computational models{{cite journal |doi=10.1093/nar/gkr1097 |title=Identifiers.org and MIRIAM Registry: Community resources to provide persistent identification |year=2011 |last1=Juty |first1=N. |last2=Le Novere |first2=N. |last3=Laibe |first3=C. |journal=Nucleic Acids Research |volume=40 |pages=D580–6 |pmid=22140103 |issue=Database issue |pmc=3245029}}[http://www.ebi.ac.uk/miriam/main/mdb?section=browse&data=MIR:00000038 SABIO-RK as part of MIRIAM Registry]
SABIO-RK Database Access
References
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External References
- [http://sabio.h-its.org/ SABIO-RK homepage]
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