SABIO-RK: Access to Biochemical Reaction Kinetics Data

Abstract

SABIO-RK (http://sabio.h-its.org/) is a curated database for biochemical reaction kinetics data drawn from different sources: from literature or direct submission by experimenters. The system offers standardized data by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. SABIO-RK can be accessed either manually via a web-based search interface or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language) complying with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. New RESTful web services, as well as a new browser interface both offer extended functionality, such as hierarchical search for data based on organism taxonomy or tissue and cell type ontology.SABIO-RK facilitates the exchange of kinetic data between experimentalists and modelers, and thereby supports the setup of quantitative computer models. The web services and the degree of data integration make it well suited for its integration into applications using or requiring kinetic data, such as systems biology modeling platforms.