Translation

The SBGN Palette (introduced in yEd since the 3.17.1 release) offers direct representation of the SBGN elements in the yEd Graph Editor format.

Table 1. SBGN PD elements and their representation in the yEd SBGN Palette

SBGN element	Representation in the yEd SBGN Palette	Encoding in the yEd GraphML format
compartment	the Compartment shape	y:GroupNode
complex	the Complex shape	com.yworks.sbgn.Complex
macromolecule	the Macromolecule shape	com.yworks.sbgn.Macromolecule
multimer simple chemical	the Simple Chemical Multimer shape	The multimer variants of the simple chemical, macromolecule, complex, nucleic acid feature classes are denoted using the “com.yworks.sbgn.style.mcount” attribute attached to the main class.
multimer macromolecule	the Macromolecule Multimer shape
multimer complex	the Complex Multimer shape
multimer nucleic acid feature	the Nucleic Acid Feature shape
nucleic acid feature	the Nucleic Acid Feature shape	com.yworks.sbgn.NucleicAcidFeature
AND	the AND Operator shape	com.yworks.sbgn.Operator The SBGN operator class is stored as the node label in yEd SBGN Palette.
NOT	the NOT Operator shape
OR	the OR Operator shape
omitted process	the Omitted Process shape	a regular process shape with double backslashes as its label
perturbing agent	the Perturbing Agent shape	com.yworks.sbgn.PerturbingAgent
phenotype	the Phenotype shape	com.yworks.sbgn.Phenotype
process	the Phenotype shape	com.yworks.sbgn.Phenotype
phenotype	the Process shape	com.yworks.sbgn.Process
simple chemical	the Simple Chemical shape	com.yworks.sbgn.SimpleChemical
source sink	the Source/Sink shape	com.yworks.sbgn.EmptySet
state variable	the State Variable shape	com.yworks.sbgn.StateVariable
submap	the Submap shape	com.yworks.sbgn.Submap
(left-oriented) tag	the (left-oriented) Tag shape	com.yworks.sbgn.Tag
(right-oriented) tag	the (right-oriented) Tag shape	com.yworks.sbgn.Tag with the com.yworks.sbgn.style.inverse attribute set to true
unit of information	the Unit of Information shape	com.yworks.sbgn.UnitOfInformation
unspecified entity	the Unspecified Entity	com.yworks.sbgn.UnspecifiedEntity
uncertain process	the Uncertain Process shape	a regular process shape with a question mark as its label
catalysis	the Catalysis edge	a line with the end equal to a white circle
consumption	the Consumption edge	a simple line
inhibition	the Inhibition edge	an line with the end equal to a T-shape
modulation	the Modulation edge	an arrow with the head equal to a white diamond
necessary stimulation	the Necessary Stimulation edge	an arrow with the head equal to a white delta and a bar
production	the Production edge	a regular arrow
stimulation	the Stimulation edge	an arrow with the head equal to a white delta

However, several SBGN elements do not have a specific correspondent in yEd SBGN Palette and we applied the following translation rules (also included in the Limitations page):

Translation from SBGN to yEd GraphML:

• complex formation and dissociation (black dots and white dots) were transformed into the generic process.