Talk at Biocuration Conference


SABIO-RK will be presented in a lightning talk at the 16th Annual International Biocuration Conference on April 24-26, 2023 in Padua (Italy).

The presentation will highlight the new visualization of SABIO-RK data published recently:

Dorotea Dudaš, Ulrike Wittig, Maja Rey, Andreas Weidemann, Wolfgang Müller
Improved insights into the SABIO-RK database via visualization
Volume 2023 (2023) baad011

SABIO-RK paper in "Database"


The new visualization of SABIO-RK data is now published in the Database Journal.

To get a better overview about the multidimensional and complex data in SABIO-RK we developed a variety of visualization concepts in the SABIO-RK user interface. We use a heat map, parallel coordinates and scatter plots to allow the interactive visual exploration of general entry-based information of biochemical reactions and specific kinetic parameter values.

Dorotea Dudaš, Ulrike Wittig, Maja Rey, Andreas Weidemann, Wolfgang Müller
Improved insights into the SABIO-RK database via visualization
Volume 2023 (2023) baad011

EnzymeML in Nature Methods


A Paper about EnzymeML serving as a seamless communication channel between experimental, modeling, and publication platforms published in Nature Methods. SABIO-RK integrates kinetic data from the EnzymeML data flow.

Lauterbach S, Dienhart H, Range J, Malzacher S, Spöring JD, Rother D, Pinto MF, Martins P, Lagerman CE, Bommarius AS, Høst AV, Woodley JM, Ngubane S, Kudanga T, Bergmann FT, Rohwer JM, Iglezakis D, Weidemann A, Wittig U, Kettner C, Swainston N, Schnell S, Pleiss J.
EnzymeML: seamless data flow and modeling of enzymatic data.
Nat Methods. 2023 Feb 9.

More details in the HITS News

SABIO-RK understands EnzymeML


In the last years we collaborated with Jürgen Pleiss and others on the development of EnzymeML - a markup language that represents a data exchange format for biocatalysis and enzymology.
As a case study the extraction and storage of data described by EnzymeML documents was implemented in the SABIO-RK workbench.
The full paper can be found here The FEBS Journal 289(2022) 5864–5874

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

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.