Additional SBO reaction annotations that could skip mass balance tests

[BenjaSanchez]

Problem description

As discussed in https://github.com/SysBioChalmers/yeast-GEM/issues/137, there are certain SBO terms that could be an indicator for memote to skip assessing the corresponding reactions in terms of mass-balance / stoichiometry consistency:

• Encapsulating process: parent of biomass pseudoreaction, "An aggregation of interactions and entities into a single process". http://www.ebi.ac.uk/sbo/main/SBO:0000395

• Pseudoreaction: "A conceptual process used for modeling purposes, often created solely to complete model structure, with respect to providing inflow or outflow of matter or material. Unlike other reactions, pseudoreactions are not usually subjected to mass balance considerations." http://www.ebi.ac.uk/sbo/main/SBO:0000631

Would any of these two (or both) make sense to include in the skipping heuristic for reactions?

[Midnighter]

• In my opinion SBO:0000631 is a perfect candidate for reactions that we should skip.
• To me, SBO:0000395 requires some clarification from the maintainers of the SBO. Both children of the term describe inherently unbalanced reactions, however, "An aggregation of interactions and entities into a single process" does not directly imply imbalance. For example, an entire pathway condensed into one reaction should clearly be balanced. Disclaimer: I don't know the SBO well enough to say if there might be a better term for my example.