SABIO-Reaction Kinetics Database

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SABIO-RK Database
Database.png
Content
Description Database for biochemical reactions and their kinetic properties
Data types
captured
Quantitative information on reaction dynamics
Organisms all
Contact
Research center Heidelberger Institut für Theoretische Studien
Laboratory Scientific Databases and Visualization
Release date 2006
Access
Website http://sabio.h-its.org
Web service URL http://sabio.h-its.org/layouts/content/webservices.gsp
Miscellaneous
License http://sabio.h-its.org/layouts/content/termscondition.gsp
Curation policy 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.[1][2][3][4]

Content of SABIO-RK Database[edit]

The data stored in SABIO-RK in a comprehensive manner is 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, and PubMed.
Currently SABIO-RK contains more than 52.000 curated single entries, for example 42% of them are related to the kinetic law type Michaelis-Menten kinetics, more than 14% of the entries contain diverse types of inhibitions. Kinetic parameters in SABIO-RK include more than 41.700 velocity constants (Vmax, kcat, rate constants), more than 42.500 Km values (including S_half for Hill equations) and about 11.800 inhibition constants (Ki, IC50). Kinetic data are available for about 850 organisms, 6.700 different reactions and about 1.480 enzymes catalysing these reactions (as of December 2015).
Several tools, databases and workflows in Systems Biology make use of SABIO-RK biochemical reaction data by integration into their framework including SYCAMORE,[5] MeMo-RK,[6] CellDesigner,[7] PeroxisomeDB,[8] Taverna workflows or tools like KineticsWizard software for data capture and analysis.[9] Additionally, SABIO-RK is part of MIRIAM registry, a set of guidelines for the annotation and curation of computational models[10][11]

Database Access[edit]

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

Pathways can be exported to SBML. A prototype for export to BioPAX/SBPAX is being prepared for release.

References[edit]

  1. ^ Wittig, Ulrike; Golebiewski, Martin; Kania, Renate; Krebs, Olga; Mir, Saqib; Weidemann, Andreas; Anstein, Stefanie; Saric, Jasmin; Rojas, Isabel (2006). "Data Integration in the Life Sciences". Lecture Notes in Computer Science. 4075: 94–103. doi:10.1007/11799511_9.  |chapter= ignored (help)
  2. ^ 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. 
  3. ^ Wittig, U.; Kania, R.; Golebiewski, M.; Rey, M.; Shi, L.; Jong, L.; Algaa, E.; Weidemann, A.; et al. (2011). "SABIO-RK--database for biochemical reaction kinetics". Nucleic Acids Research. 40 (Database issue): D790–6. doi:10.1093/nar/gkr1046. PMC 3245076Freely accessible. PMID 22102587. 
  4. ^ Müller W. In: Pfade im Informationsdschungel Spektrum der Wissenschaft, Spektrum Spezial: Datengetriebene Wissenschaft, December 2011
  5. ^ 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". Bioinformatics. 24 (12): 1463–4. doi:10.1093/bioinformatics/btn207. PMID 18463116. 
  6. ^ 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. doi:10.1111/j.1742-4658.2010.07778.x. PMID 20738395. 
  7. ^ 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. 
  8. ^ Schluter, A.; Real-Chicharro, A.; Gabaldon, T.; Sanchez-Jimenez, F.; Pujol, A. (2009). "PeroxisomeDB 2.0: An integrative view of the global peroxisomal metabolome". Nucleic Acids Research. 38 (Database issue): D800–5. doi:10.1093/nar/gkp935. PMC 2808949Freely accessible. PMID 19892824. 
  9. ^ Messiha, Hanan L.; Malys, Naglis; Carroll, Kathleen M. (2011). "Methods in Systems Biology". Methods in Enzymology. 500: 215–231. doi:10.1016/B978-0-12-385118-5.00012-8. ISBN 978-0-12-385118-5.  |chapter= ignored (help)
  10. ^ Juty, N.; Le Novere, N.; Laibe, C. (2011). "Identifiers.org and MIRIAM Registry: Community resources to provide persistent identification". Nucleic Acids Research. 40 (Database issue): D580–6. doi:10.1093/nar/gkr1097. PMC 3245029Freely accessible. PMID 22140103. 
  11. ^ SABIO-RK as part of MIRIAM Registry

External References[edit]