New Visualization in SABIO-RK


In order to facilitate interactive search and data refinement through the SABIO-RK data, a new visualization module is developed. Its goal is to improve the understanding of the database content and detect possible discrepancies between kinetic parameters from different publication sources. It is meant to support both modellers and experimentalists to extract the highest possible amount of information from accumulated and orderly presented data. Clustering and grouping of the data (e.g. kinetic parameters, EC numbers, environmental conditions) is implemented.

Reactions, proteins/enzymes, organisms, tissues and experimental conditions (pH and temperature) are included within three different visualization concepts representing a heat map overview, parallel coordinates and a scatter plot matrix with histograms. Since each database entry can contain several kinetic parameters (with its types, values, units and associated species) they are shown in two separate visualizations. This improves the possibilities of exploring the kinetic data and its connections to the rest of the data in SABIO-RK. Data can be visually adjusted by determining what exactly is shown within the graphs, by reordering the data and by selecting different color schemes for the visualizations using the user interface.

The new visualizations enable navigating through the database without the need to know much about available keywords in the database or about manually composing search queries.

Poster at COMBINE and ICSB


The new visualization of SABIO-RK data including kinetic parameters is presented by Dorotea Dudaš at the COMBINE 2022 and at the International Conference on Systems Biology (ICSB) in Berlin in October 2022.

Poster title: Deep insight into SABIO-RK data via visualization
Authors: Dorotea Dudaš, Maja Rey, Ulrike Wittig, Andreas Weidemann, Wolfgang Müller