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ModelSEED / ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
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Placeholder issue for decisions regarding use of reaction identifiers in ModelTemplate #18

Closed samseaver closed 7 years ago

samseaver commented 8 years ago

I'm currently starting to re-build the Plant ModelTemplate. Its not so much that I'm changing the list of reactions, but I'm changing how compartmentalization is assigned to reactions, as there'll be some manual curation to that effect.

I'm doing this with the current version of the ModelTemplate, pending any changes made to the new version that'll be published with ProbModelSEED, but it serves a way for me to organize the data in the meantime.

But the whole point of this issue is that I'm also bearing in mind that we're working towards a unified and compartment-free biochemistry, and as such, I'm trying to anticipate which reaction identifiers I should use.

In the case where two identical reactions are otherwise in different compartments, I will use the reaction id with the lowest number. In the ModelTemplate, I will create duplicate template reactions, but otherwise assign different compartments.

To an extent, this is obvious, but I wanted to be explicit about it.

JamesJeffryes commented 7 years ago

Hey Sam, can I close this as an issue as it something that you've already done?

samseaver commented 7 years ago

Yes.