(2) "SBML layout"<->"SBGN PD":
(3) "SBML qual"<->"SBGN AF":
Mapping (3) still needs some work, the values of Input and Output still needs to be mapped somehow, although I am not sure how to proceed.
Could anyone give me some feedback to the 3 mappings please? Are there anything unclear, are there mistakes?
I am working on mapping (4), but I am stuck because it is unclear how I should represent SBGN AF glyphs using SBML core alone.
I have 2 options for "SBGN AF" -> "SBML core":
 use SBML AssignmentRule to map SBGN "Modulation arcs"+"Logical operators"
 use SBML KineticLaw to map SBGN "Modulation arcs"+"Logical operators"
In the case of , SBGN "Activity nodes" map to Species, and Species initialAmount take on value of a Parameter, which is associated with an InitialAssignment.
The resulting value of an Activity Flow would be calculated using an AssignmentRule, where the Math calculates values provided in the Species, and produce a boolean. This boolean value would determine whether to change the value of the resulting "Biological activity" or "Phenotype".
In the case of , the approach would be similar, but I feel that by using a KineticLaw, I am forced to create a Reaction between the Input and Output Species, which makes the mapping look like "SBGN PD" -> "SBML core". I think "SBGN AF" should not map to any Reactions, because we cannot assume a Reaction exists for an Activity Flow model. AF is supposed to represent activities without knowing the details of the intermediate steps.
Also, I do not know whether mapping of "SBML core" -> "SBGN AF" would be possible, because I assume the "SBML core" model would be quantitative. Converting from a quantitative model to a qualitative SBGN AF could be incompatible. Under what circumstances would a "SBML core" -> "SBGN AF" be feasible?
Thank you for your help!