cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK

Abstract:

Kinetic data of biochemical reactions are essential for the creation of kinetic models of biochemical networks. One of the main resources of such information is SABIO-RK, a curated database for kinetic data of biochemical reactions and their related information. Despite the importance for computational modelling there has been no simple solution to visualize the kinetic data from SABIO-RK.
In this work, I present cy3sabiork, an app for querying and visualization of kinetic data from SABIO-RK in Cytoscape. The kinetic information is accessible via a combination of graph structure and annotations of nodes, with provided information consisting of: (I) reaction details, enzyme and organism; (II) kinetic law, formula, parameters; (III) experimental conditions; (IV) publication; (V) additional annotations. cy3sabiork creates an intuitive visualization of kinetic entries in form of a species-reaction-kinetics graph, which reflects the reaction-centered approach of SABIO-RK. Kinetic entries can be imported in SBML format from either the SABIO-RK web interface or via web service queries. The app allows for easy comparison of kinetic data, visual inspection of the elements involved in the kinetic record and simple access to the annotation information of the kinetic record.
I applied cy3sabiork in the computational modelling of galactose metabolism in the human liver.

Author: Matthias König

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König, M. (2016). cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK. F1000Research, 5, 1736. http://doi.org/10.12688/f1000research.9211.1
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Created: 18th Jul 2016 at 18:18

Last updated: 18th Jul 2016 at 18:21

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