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segrelab / escher-maps

Universal ModelSEED Escher maps
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Decide on compartment nomenclature #6

Closed hgscott closed 1 year ago

hgscott commented 1 year ago

All the reactions/metabolites in the ModelSEED database are NOT compartment-specific (i.e. rxn00001), but in models, they are (i.e. rxn0001_c0). We want to have a standard way to mark compartments so that these maps work for all of our models.

hgscott commented 1 year ago

All of the KBase models I can find use (i.e. all the ones I made of ALT) use _c0 and _e0. None of those have a periplasm compartment, I don't know if/when KBase would add that.