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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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Some reactions don't have reactants and/or products #42

Closed JamesJeffryes closed 5 years ago

JamesJeffryes commented 7 years ago

From @smoretti on October 7, 2016 14:17

Hi

Some reactions don't have reactants and products. E.g.

Some reactions don't have reactants or products. E.g.

Copied from original issue: ModelSEED/ModelSEED-UI#55

JamesJeffryes commented 7 years ago

From @samseaver on October 7, 2016 15:2

Hi Sebastien, I'm responsible for maintaining the master list of reactions and compounds at ModelSEEDDatabase, but I haven't been updating the databases that are reached using the ModelSEED API.

But to compound things, there are probably several ways in which you can do so, can you let me know which repository you are using for the API, and which URLs you are using to instantiate the service?

Thanks Sam

JamesJeffryes commented 7 years ago

From @smoretti on October 7, 2016 15:17

I use https://www.patricbrc.org/api/model_compound and https://www.patricbrc.org/api/model_reaction The same URLs used on the ModelSeed.org web site

samseaver commented 5 years ago

We balance out identical reactants and products, so if a compound is on both side of the equations, and in the same compartment, we remove it. The end result means that some reactions are either empty or one-sided, but, if this were the case, they would've been unusable for metabolic modeling anyway.