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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Get pathways/subsystems #32

Closed lcottret closed 3 years ago

lcottret commented 5 years ago

Most often in the models, reactions are classified into pathways or subsystems. It would be convenient to get this information in the SBML (or in a tabulated file) produced by carveme.

cdanielmachado commented 5 years ago

Thanks for the suggestion, this is definitely something very useful to have, and it is in our plans.

Unfortunately, the BiGG database does not integrate the pathway information from the different models, nor is there a standardized nomenclature to classify the pathways.

One solution would be to merge all pathway information for each reaction from all available models, but the result would probably be a mess. We will try to find a better solution until our next update release.

lipme commented 3 years ago

Hi ! Closed : this means that this feature is in the new version :-) ? Regards, Ludo

cdanielmachado commented 3 years ago

Sorry, I should have left a comment. :)

Unfortunately not. I closed the issue because I dropped this feature from the priorities in our roadmap. At least for now.