SABIO-Reaction Kinetics Database
SABIO-RK ( S ystem for the A nalysis of bio chemical pathways - R eAction K inetics) is a web-accessible database which complete information on biochemical reactions and their kinetic stores properties.
In contrast to other databases, which are either an enzyme database ( BRENDA ) or a protein database ( UniProt ) or a model database (BioModels, JWS Online), SABIO-RK represents a reaction-oriented database with quantitative information on reaction dynamics.
The dynamics of biochemical reactions are of central importance in biology and medicine for the understanding of cellular processes and for the development of drugs. The experimentally obtained data for the quantitative description of reaction dynamics and enzyme kinetics are extracted manually from the literature and saved in standardized form in SABIO-RK. The content of the database includes kinetic parameters related to biochemical reactions and their biological sources. In addition, the kinetic rate rates of enzymes and the corresponding equations and the associated experimental conditions are stored. All data is manually curated and commented by biological experts, supported by automated consistency checks. SABIO-RK can be accessed via web-based user interfaces or automatically via web services. Both interfaces support the export of the data together with the corresponding annotations in SBML (Systems Biology Markup Language) , for example for the import into modeling tools. SABIO-RK is maintained and further developed at the Heidelberg Institute for Theoretical Studies (HITS) .
Currently, more than 60,000 individual kinetic data sets are stored in SABIO-RK, which come from over 6,000 publications (as of September 2019). Annotations are made to a number of other databases, including KEGG , ChEBI , PubChem , UniProt , NCBI , Reactome , BRENDA , MetaCyc , BioModels , and PubMed .
Access to SABIO-RK
The use of SABIO-RK is free of charge for academic and non-commercial users. Commercial users need a license. The stored data can be accessed in various ways:
- Web-based (browser): the database can be searched for kinetic data using various criteria. These criteria include a. the search for substrates , products, coenzymes , inhibitors , enzyme names , EC numbers , tissues , organisms , publications , kinetic parameter types , cellular localizations or metabolic pathways .
- In addition, web services are made available which forward the kinetic information on automated request ( REST- compliant interfaces).
credentials
- ^ U Wittig, M Rey, A Weidemann, R Kania, W Müller: SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. . In: Nucleic acids research . 46, No. D1, January 4, 2018, pp. D656-D660. doi : 10.1093 / nar / gkx1065 . PMID 29092055 .
- ↑ U Wittig, R Kania, M Golebiewski, M Rey, L Shi, L Jong, E Algaa, A Weidemann, H Sauer-Danzwith, S Mir, O Krebs, M Bittkowski, E Wetsch, I Rojas, W Müller: SABIO- RK - database for biochemical reaction kinetics. . In: Nucleic acids research . 40, No. Database issue, January 2012, p. D790-6. doi : 10.1093 / nar / gkr1046 . PMID 22102587 .
- ↑ I Rojas, M Golebiewski, R Kania, O cancer, S Me A Weidemann, U Wittig: Storing and annotating of kinetic data . In: In Silico Biology . 7, No. 2 Suppl, 2007, pp. S37-44. PMID 17822389 .
- ↑ Ulrike Wittig, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Stefanie Anstein, Jasmin Saric, Isabel Rojas: SABIO-RK: Integration and Curation of Reaction Kinetics Data . In: Data Integration in the Life Sciences (= Lecture Notes in Computer Science), Volume 4075 2006, ISBN 978-3-540-36593-8 , pp. 94-103, doi : 10.1007 / 11799511_9 .
- ^ W. Müller: Paths in the information jungle . In: Spectrum of Science , Spectrum Special: Data-Driven Science, December 2011.