Closed gregmedlock closed 5 years ago
I understand this is an old comment, I apologize for never having replied. We were in a transition from using letters for original compartments to using numbers for generic compartments. We no longer store the original compartments in the biochemistry (in the new reactions.tsv) but do try to capture them in the template files.
Thanks for the update! New approach looks nice/clean, btw.
The compartment indices specified in compartments.master.tsv and compartments.default.tsv don't match those in reactions.master.tsv (or any reaction DB file, for that matter). The reaction DB files only contain 0, 1, and 2 for compartment indices in the equation, stoichiometry, and definition.
What the indices in the reaction DB files currently correspond to is unclear, since 1 is used interchangeably for extracellular and periplasm. 2 appears to be unique to Ton transport system reactions.