GraphML-SBGN bidirectional converter for metabolic networks

Abstract

Systems biology researchers need feasible solutions for editing and visualisation of large biological diagrams. Here, we present the ySBGN bidirectional converter that translates metabolic pathways, developed in the general-purpose yEd Graph Editor (using the GraphML format) into the Systems Biology Graphical Notation Markup Language (SBGN-ML) standard format and vice versa. We illustrate the functionality of this converter by applying it to the translation of the ReconMap resource (available in the SBGN-ML format) to the yEd-specific GraphML and back. The ySBGN tool makes possible to draw extensive metabolic diagrams in a powerful general-purpose graph editor while providing results in the standard SBGN format.

Keywords: GraphML; Recon2 human metabolic reconstruction; process description; systems biology graphical notation; systems biology standard.

Figure 1:

The SBGN process glyph versus the yEd process glyph. In black there are represented the process glyph (square box) and the ports (black line). In red there are represented the incoming and outgoing arcs. The SBGN process glyph connects to these arcs through the ports which is represented by the two black lines on each side of the square box. The representation of yEd of a process does not consider ports by default: The incoming and outgoing arcs are directly connected to the process square box.

Figure 2:

Examples of the conversion of processes in the ySBGN converter: (a) Reversible process; (b) irreversible process with horizontal orientation; (c) irreversible process with vertical orientation.

Figure 3:

The ReconMap 2 in the yEd Graph Editor. The ySBGN converter translated the ReconMap resource available in SBGN-ML format into the yEd-specific GraphML format. Information on colours and annotations is also preserved during the translation. Please note the SBGN Palette on the right side, available since the yEd 3.17.1 release.