SABIO-Reaction Kinetics Database: Difference between revisions

Edit links
From Wikipedia, the free encyclopedia
Browse history interactively
← Previous editNext edit →
Content deleted Content added
VisualWikitext
Cleanup
No edit summary
Line 30: Line 30:
as well as kinetic law and parameter types and experimental and environmental conditions under which the kinetic data were determined.
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 [[Metabolic_pathway|pathways]] including their [[Reagent|reaction participants]],
Additionally, SABIO-RK contains information about the underlying biochemical reactions and [[Metabolic_pathway|pathways]] including their [[Reagent|reaction participants]],
[[Cell_(biology)|cellular]] location and detailed information about the [[Enzymes|enzymes]] catalysing the reactions
[[Cell_(biology)|cellular]] location and detailed information about the [[Enzymes|enzymes]] catalysing the reactions<ref>{{cite journal |doi=11799511_9 10.1007/11799511_9}}</ref><ref>{{cite journal |pmid=17822389}}</ref><ref>{{cite journal |doi=10.1093/nar/gkr1046}}</ref><ref>Müller W. In:
<ref>Wittig U, Golebiewski M, Kania R, Krebs O, Mir S, Weidemann A, Anstein S, Saric J, Rojas I. In: [http://www.springerlink.com/content/kw1kv13614272400/?p=9b9a98e3b7c04ec189cd2927fcc83808&pi=8 SABIO-RK: Integration and Curation of Reaction Kinetics Data] Proceedings of the 3rd International workshop on Data Integration in the Life Sciences 2006 (DILS'06). Hinxton, UK. Lecture Notes in Bioinformatics, 4075:94-103(2006). [[Digital_object_identifier|doi]] [http://dx.doi.org/10.1007/11799511_9 10.1007/11799511_9]</ref>
<ref>Rojas I, Golebiewski M, Kania R, Krebs O, Mir S, Weidemann A, Wittig U. In: [http://www.bioinfo.de/isb/200707S105/ Storing and annotating of kinetic data] In Silico Biol. 2007, 7(2 Suppl), 37-44. [[PubMed_Identifier|PMID]] [http://www.ncbi.nlm.nih.gov/pubmed/17822389 17822389]</ref>
<ref>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. In:
[http://nar.oxfordjournals.org/content/early/2011/11/17/nar.gkr1046.short?rss=1 SABIO-RK—database for biochemical reaction kinetics] Nucleic Acids Res. 40, Database issue, 2012, D790-6.
[[Digital_object_identifier|doi]] [http://dx.doi.org/10.1093/nar/gkr1046 10.1093/nar/gkr1046] [[PubMed_Identifier|PMID]] [http://www.ncbi.nlm.nih.gov/pubmed/22102587 22102587]</ref>
<ref>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</ref>.
[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</ref>.


Line 43: Line 37:
Currently SABIO-RK contains more than 42.000 curated single entries, for example 38% of them are related to the kinetic law type [[Michaelis–Menten_kinetics|Michaelis-Menten kinetics]], more than 14% of the entries contain diverse types of inhibitions. Kinetic parameters in SABIO-RK include more than 27.300 velocity constants (V<sub>max</sub>, [[Turnover_number|k<sub>cat</sub>]], [[Reaction_rate_constant|rate constants]]), more than 30.900 K<sub>m</sub> values (including S_half for [[Hill_equation_(biochemistry)|Hill equations]]) and about 7.300 [[Enzyme_inhibitor|inhibition constants]] (Ki, IC50). Kinetic data are available for about 660 organisms, 7.300 different reactions and almost 1.000 enzymes catalysing these reactions (as of October 2011).<br/>
Currently SABIO-RK contains more than 42.000 curated single entries, for example 38% of them are related to the kinetic law type [[Michaelis–Menten_kinetics|Michaelis-Menten kinetics]], more than 14% of the entries contain diverse types of inhibitions. Kinetic parameters in SABIO-RK include more than 27.300 velocity constants (V<sub>max</sub>, [[Turnover_number|k<sub>cat</sub>]], [[Reaction_rate_constant|rate constants]]), more than 30.900 K<sub>m</sub> values (including S_half for [[Hill_equation_(biochemistry)|Hill equations]]) and about 7.300 [[Enzyme_inhibitor|inhibition constants]] (Ki, IC50). Kinetic data are available for about 660 organisms, 7.300 different reactions and almost 1.000 enzymes catalysing these reactions (as of October 2011).<br/>
Several tools, databases and workflows in [[Systems_biology|Systems Biology]] make use of SABIO-RK biochemical reaction data by integration into their framework including
Several tools, databases and workflows in [[Systems_biology|Systems Biology]] make use of SABIO-RK biochemical reaction data by integration into their framework including
SYCAMORE,<ref>{{cite journal |doi=10.1093/bioinformatics/btn207}}</ref>
SYCAMORE<ref>Weidemann A, Richter S, Stein M, Sahle S, Gauges R, Gabdoulline R, Surovtsova I, Semmelrock N, Besson B, Rojas I, Wade R, Kummer U. In: [http://bioinformatics.oxfordjournals.org/content/24/12/1463.long SYCAMORE-a systems biology computational analysis and modeling research environment] Bioinformatics 2008, 24, 1463-4. [[Digital_object_identifier|doi]] [http://dx.doi.org/10.1093/bioinformatics/btn207 10.1093/bioinformatics/btn207] [[PMID#PubMed_identifier|PMID]] [http://www.ncbi.nlm.nih.gov/pubmed/18463116 18463116]</ref>,
MeMo-RK,<ref>{{cite journal |doi=10.1111/j.1742-4658.2010.07778.x}}</ref>
MeMo-RK<ref>Swainston N, Golebiewski M, Messiha HL, Malys N, Kania R, Kengne S, Krebs O, Mir S, Sauer-Danzwith H, Smallbone K, Weidemann A, Wittig U, Kell DB, Mendes P, Müller W, Paton NW, Rojas I. In: [http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2010.07778.x/abstract Enzyme kinetics informatics: from instrument to browser] FEBS J. 2010, 277, 3769-79. [[Digital_object_identifier|doi]] [http://dx.doi.org/10.1111/j.1742-4658.2010.07778.x 10.1111/j.1742-4658.2010.07778.x] [[PMID#PubMed_identifier|PMID]] [http://www.ncbi.nlm.nih.gov/pubmed/20738395 20738395]</ref>,
CellDesigner,<ref>{{cite journal |pmid=17822394}}</ref>
CellDesigner<ref>Funahashi A, Jouraku A, Matsuoka Y, Kitano H. In: [http://www.bioinfo.de/isb/200707S110 Integration of CellDesigner and SABIO-RK] In Silico Biol. 2007(2 Suppl), 81-90. [[PMID#PubMed_identifier|PMID]] [http://www.ncbi.nlm.nih.gov/pubmed/17822394 17822394]</ref>,
PeroxisomeDB<ref>Schlüter A, Real-Chicharro A, Gabaldón T, Sánchez-Jiménez F, Pujol A. In: [http://nar.oxfordjournals.org/content/38/suppl_1/D800.long PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome] FEBS J. 2010, 277, 3769-79. [[Digital_object_identifier|doi]] [http://dx.doi.org/10.1093/nar/gkp935 10.1093/nar/gkp935] [[PMID#PubMed_identifier|PMID]] [http://www.ncbi.nlm.nih.gov/pubmed/19892824 19892824]</ref>,
PeroxisomeDB<ref>Schlüter A, Real-Chicharro A, Gabaldón T, Sánchez-Jiménez F, Pujol A. In: [http://nar.oxfordjournals.org/content/38/suppl_1/D800.long PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome] FEBS J. 2010, 277, 3769-79. [[Digital_object_identifier|doi]] [http://dx.doi.org/10.1093/nar/gkp935 10.1093/nar/gkp935] [[PMID#PubMed_identifier|PMID]] [http://www.ncbi.nlm.nih.gov/pubmed/19892824 19892824]</ref>,
Taverna workflows<ref>Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW. In: [http://www.biomedcentral.com/1471-2105/11/582 Systematic integration of experimental data and models in systems biology] BMC Bioinformatics 2010, 11, 582. [[Digital_object_identifier|doi]] [http://dx.doi.org/10.1186/1471-2105-11-582 10.1186/1471-2105-11-582] [[PMID#PubMed_identifier|PMID]] [http://www.ncbi.nlm.nih.gov/pubmed/2111484 2111484]</ref>
Taverna workflows<ref>Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW. In: [http://www.biomedcentral.com/1471-2105/11/582 Systematic integration of experimental data and models in systems biology] BMC Bioinformatics 2010, 11, 582. [[Digital_object_identifier|doi]] [http://dx.doi.org/10.1186/1471-2105-11-582 10.1186/1471-2105-11-582] [[PMID#PubMed_identifier|PMID]] [http://www.ncbi.nlm.nih.gov/pubmed/2111484 2111484]</ref>

Revision as of 21:31, 11 February 2012

SABIO-RK Database
Content
DescriptionA database storing information about biochemical reactions and their kinetic properties
Data types
captured		Quantitative information on reaction dynamics
Organismsall
Contact
Research centerHeidelberger Institut für Theoretische Studien
LaboratoryScientific Databases and Visualization
Release date2006
Access
Websitehttp://sabio.h-its.org
Web service URLhttp://sabio.h-its.org/webservice.jsp
Miscellaneous
Licensehttp://sabio.h-its.org/license.html
Curation policyCurated 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

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 42.000 curated single entries, for example 38% 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 27.300 velocity constants (Vmax, kcat, rate constants), more than 30.900 Km values (including S_half for Hill equations) and about 7.300 inhibition constants (Ki, IC50). Kinetic data are available for about 660 organisms, 7.300 different reactions and almost 1.000 enzymes catalysing these reactions (as of October 2011).
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[9] 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]

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
  • SOAP- and RESTful-based web services for programmatic access

References

  1. ^ . doi:11799511_9 10.1007/11799511_9. {{cite journal}}: Check |doi= value (help); Cite journal requires |journal= (help); Missing or empty |title= (help)
  2. ^ . PMID 17822389. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)
  3. ^ . doi:10.1093/nar/gkr1046. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)
  4. ^ Müller W. In: Pfade im Informationsdschungel Spektrum der Wissenschaft, Spektrum Spezial: Datengetriebene Wissenschaft, December 2011
  5. ^ . doi:10.1093/bioinformatics/btn207. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)
  6. ^ . doi:10.1111/j.1742-4658.2010.07778.x. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)
  7. ^ . PMID 17822394. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)
  8. ^ Schlüter A, Real-Chicharro A, Gabaldón T, Sánchez-Jiménez F, Pujol A. In: PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome FEBS J. 2010, 277, 3769-79. doi 10.1093/nar/gkp935 PMID 19892824
  9. ^ Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW. In: Systematic integration of experimental data and models in systems biology BMC Bioinformatics 2010, 11, 582. doi 10.1186/1471-2105-11-582 PMID 2111484
  10. ^ Messiha HL, Malys N, Carroll KM. In: Towards a full quantitative description of yeast metabolism a systematic approach for estimating the kinetic parameters of isoenzymes under in vivo like conditions Methods Enzymol. 500, 2011, 215-231. doi 10.1016/B978-0-12-385118-5.00012-8 PMID 21943900
  11. ^ Juty N, Le Novère N, Laibe C. In: Identifiers.org and MIRIAM Registry: community resources to provide persistent identification Nucleic Acids Res. 2010, 40(Database issue), D580-6. doi 10.1093/nar/gkr1097 PMID 22140103
  12. ^ SABIO-RK as part of MIRIAM Registry

External References

Retrieved from "https://en.wikipedia.org/w/index.php?title=SABIO-Reaction_Kinetics_Database&oldid=476341648"