Best practices of drawing reversible enzyme-catalyzed reactions

[draeger]

In the past, the SBGN editors decided that drawing catalysis of reversible reactions was not permissible, as it can often be hardly distinguished which direction is favored by the catalysis. As it stands right now, the process should be duplicated in two irreversible processes, each one catalyzed by the enzyme. While the arguments for this are pretty clear and reasonable, it should be changed to a recommendation of best practices for the sake of usability.

Rationale: It can be expected that (a fraction of) users of SBGN will draw reversible arcs anyway for this. If SBGN software is restrictive and does not allow for reversible catalyzed reactions, users will be frustrated and go to Illustrator or other tools or even stop using SBGN at all and use another representation format in which they can draw this most easily. Furthermore, the preferred direction of catalysis may depend on the current state of the system, following Le Chatelier's principle, and can therefore dynamically change.

As a best practice, the specification would explain the rationale of splitting reversible catalyzed reactions and encourage drawing it this way. Furthermore, a validator could raise a warning when encountering this in an SBGN-ML graph. But users would still have the freedom to represent it in their favorite way.

[hasanbalci]

@draeger If you're referring to reversible reactions that are symmetrically modulated (like catalysis), then the specification allows it already since it is referring to separation for only asymmetric modulations in Section 2.6.1 Glyph: Process.

[cannin]

This issue does not arise when the reaction is symmetric see Figure 2.26