SABIO-RK database

6. November 2014

Biochemical Reaction Kinetics Database

SABIO-RK (http://sabio.h-its.org) is a curated database containing structured information about biochemical reactions and their corresponding kinetics. It describes participants and modifiers of the reactions, as well as measured kinetic data (including kinetic rate equations) embedded in their experimental and environmental context. The system offers standardized data for metabolic and newly also signaling reactions by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. It enables the access to kinetic data for experimentalists and modellers. Thereby, SABIO-RK facilitates the exchange of the data between experimentalists and modellers, supporting the setup of quantitative computer models.

The data in SABIO-RK is either manually extracted from published literature or directly submitted by experimenters. It is curated by experts and supplemented with additional information from other databases and biological ontologies. The database can be accessed either manually via a web-based search interface or via web services that allow direct automated access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology MarkupLanguage) complying with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. Confidential data, such as directly submitted pre-publication data, can be hidden for public access by defining the sharing rights for named users.