vessel_id should not be a mandatory field in AbstractSpecies

[haeussma]

To my understanding the purpose of the different species definitions in EnzymeML is to add information on a species regardless of its context in a reaction. Thus, the mandatory link to a reaction vessel makes no sense imo.
However, I think the link to the vessel is important and should be linked in the Measurement section. This would allow to define different vessels without the need to set up all species multiple times for each vessel.

Any opinions on that?

[JR-1991]

I see what you mean. We had to add it at the Reactant level to ensure we comply with the SBML requirements. So that you know, the compartment_id field of a species object is mandatory in SBML. On the other hand, we don't really use the vessel_id field that much in EnzymeML. If a vessel_id isn't provided, we could use a placeholder value instead.

Adding the vessel to a Measurement object is a good idea. However, a vessel could potentially also be used to store a certain substance or enzyme. Hence, I would still allow it to be added to the AbstractSpecies level.