search

ModelSEED / ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
Other
53 stars 38 forks source link

compartment indices don't match reaction DB #30

Closed gregmedlock closed 5 years ago

gregmedlock commented 8 years ago

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.

samseaver commented 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.

gregmedlock commented 5 years ago

Thanks for the update! New approach looks nice/clean, btw.