Abstract

AbstractThe simulation of quantitative biochemical models not only requires qualitative information about the stoichiometry of the described networks, but also kinetic data describing their dynamics. Such kinetic data have to be experimentally measured, collected, systematically structured and stored to finally make them accessible. However, the dataflow from the experiment to the model is still a bottleneck, calling for systems that capture the data directly from the instrument, process and normalize it to agreed standards and finally transfer the data to publicly available databases.SABIO-RK (http://sabio.h-its.org) is a curated database system which we have developed for bundling data referring to biochemical reactions and their kinetics. It offers data for metabolic pathways and as a novelty also for signalling reactions. Until recently, the database solely has been compiled through manual data mining of published papers and merging the kinetic data excerpt with information collected from other databases. We have designed the novel XML-based schema SabioML for exchanging experimentally derived kinetic data and corresponding metadata between programs or databases. The schema is tailored to SABIO-RK, however also could serve for transferring data between other resources. It comprises the description of kinetic laws with their parameters and relevant metadata in a structured and standardised format applying controlled vocabulary, as well as the possibility to assign annotations complying with the MIRIAM standard (Minimum Information Required In the Annotation of Models). Based on this data description format we have developed a submission interface that allows transfer of reaction kinetics data directly from the experimental instrument to the SABIO-RK database. The data can be accessed by the submitting researcher and, after release by the submitter and curation to ensure completeness of the data, also by the public, either manually via a web-based user interface or automated via web-services, both supporting the export of the data together with its annotations in SBML (Systems Biology Mark-up Language).The system introduced here considerably facilitates the exchange of kinetic data between experimentalists and modelers. We are convinced that in systems biology it will become quite useful for the integration of the results of high throughput assays into biochemical computer models for simulation.

Highlights

  • Kinetic data from literature and directly from experiments merged with data describing biochemical reactions and pathways from other resources

  • Supports standardized annotations for many data types Compliant with the MIRIAM standard (Minimal Information Required In the Annotation of Models)

  • - JAW-WS based - Integration possible in modeling platforms or simulation tools (e.g.CellDesigner) - Cross-linking with other databases (e.g. ChEBI) - Data export in Systems Biology Markup Language (SBML) supported

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Summary

Martin Golebiewski

Data about metabolic and signalling reactions, as well as reaction mechanisms Data is unified, structured, normalized, interrelated and annotated Access through a web-based user interface and through web-services (API) Proprietary levels can be defined to restrict access to sensitive data Data export possible in Systems Biology Markup Language (SBML)

General Information
SBML export of direct submission data
Full Text
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