Editors

A brief comparison of the tools we used for editing large biological diagrams is provided in Table 1.

Table 1. Features for managing large scale biological diagrams in SBGN PD

Features	yEd	CellDesigner	SBGN-ED	Newt
Drawing directly in SBGN PD	+	-	+	+
SBGN-ML export	-	+	+	+
Large-scale diagrams	+	+	-	+
Usability: on-the-fly snap-to-line functionality	+	-	-	+
Usability: colours for lines	+	-	+	+
Accessible web version	+	-	-	+
Drawing offline	+	+	+	-

A list of available editors for biological maps in the SBGN PD language is provided in Table 2. The list is based on information provided on the SBGN website. We selected alphabetically the software with i) valid URLs for executable files and/or for source code files and/or ii) references available.

Table 2: Information on available editors for biological maps in the SBGN PD language

Editor name	Availability	Reference
BIOCHAM	http://contraintes.inria.fr/biocham/	(Jovanovska et al., 2010)
Biographer	https://code.google.com/archive/p/biographer/	(Krause et al., 2013)
CellDesigner	http://www.celldesigner.org/	(Funahashi et al., 2007)
ChiBE	https://code.google.com/archive/p/chibe/	(Babur et al., 2014)
Dunnart	https://github.com/mjwybrow/dunnart/	(Dwyer et al., 2009)
geneXplain platform	http://genexplain.com/genexplain-platform/	(Blazquez et al., 2018)
Krayon for SBGN	https://github.com/wiese42/krayon4sbgn	n/a
Netbuilder’	https://sourceforge.net/projects/apostrophe/	(Brown et al., 2002)
Newt Editor	http://newteditor.org/	n/a
PathVisio	http://www.pathvisio.org/plugin/sbgn-plugin/	(van Iersel et al., 2008)
SBGN-ED	https://immersive-analytics.infotech.monash.edu/vanted/addons/sbgn-ed/	(Czauderna et al., 2010)
SBGNTikZ	https://github.com/Adrienrougny/sbgntikz	n/a
yEd Graph Editor	https://www.yworks.com/products/yed	n/a