ModelSEED/ModelSEED — pull request #118 by devoid (2012-10-17 02:12:40+00:00)
Title: Start of model-build refactor

Trying to break down buildModelFromAnnotation made my head spin; so I need some help. I'm starting with processing Complexes given an Annotation object and generating ModelReactions.

Questions:

1. Triggering: if I have a role and the complexRole lists it as triggering, do I add all the reactions in the complex?
2. Optional: If I've triggered a reaction, when should I add the optional roles?
3. Non-triggering, non-optional: Do I add the reactions if all non-optional roles are satisfied?
4. Non-triggering, optional: Do I add these roles?

5. Notes section: Does this get populated for both the protein and subunit? One but not the other?
6. I should only add a feature to the SubunitGene section if's associated with the corresponding role?

7. Should we consider the featureRole compartment to be synonymous with a compartment id?
8. How does the featureRole compartment translate visa vi transport reactions into a model reaction?