Description of the format can be found here: http://co.mbine.org/specifications/sbgn.af.level-1.version-1.2.pdf

We already use libsbgn library for parsing SBGN: https://mvnrepository.com/artifact/org.sbgn/libsbgn/0.2

Below you can find SBGN AF mapping by Alexander:

Here is the mapping between CellDesigner's Reduced Notation links and SBGN Activity Flow links. I use exact terms from the CellDesigner's Reduced Notation palette and the terms of the Activity Flow reference card (attached).

Positive Influence -> positive influence

Reduced Physical Stimulation -> positive influence

Unknown Positive Influence -> positive influence

Unknown Reduced Physical Stimulation -> positive influence

Negative Influence -> negative influence

Unknown Negative Influence -> negative influence

Reduced Modulation -> unknown influence

Unknown Reduced Modulation -> unknown influence

Reduced Trigger -> necessary stimulation

Unknown Reduced Trigger -> necessary stimulation

In principle, the unknown (dashed lines) could be kept, it is okay not be strictly AF in this case.

Please note that, as we discussed, we should not change the way you handle the internal model in MINERVA, >we should only modify the visual part when a user checks "Visualise in SBGN Activity Flow" box.

This is the compromise we agreed on: modifying visually, not the model itself. Activity Flow is >conceptually a different language. For example, it would be tricky to try to present multiple state >variable in AF (and it is not needed, not the purpose of this language).

When it comes from CellDesigner: normal pipeline but modified visualisation for AF if a user requests it >(works only for reduced notation, no processes allowed).

When it comes from SBGN-ML, the mapping to CellDesigner Reduced Notation (or internal MINERVA model) is >possible, fewer problems there since in a clean AF we would not introduce state variables etc.

Mapping from SBGN-ML AF to CellDesigner for links:

positive influence -> Positive Influence

negative influence -> Negative Influence

unknown influence -> Reduced Modulation

necessary stimulation -> Reduced Trigger

Mapping from SBGN-ML to CellDesigner for entities: keep labels as they are, use auxiliary units to inform >on the type of shape to be used, for example, macromolecule, RNA, gene etc.