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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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External pathways #138

Closed samseaver closed 5 years ago

samseaver commented 5 years ago

@Fxe @JamesJeffryes

I've add pathways as a separate ontology in the Aliases folder and as a new 'pathways' attribute to the reactions database. The entry is similar to that for Aliases, and looks like this:

"MetaCyc:Degradation (Degradation/Utilization/Assimilation);Glyphosate-Degradation (glyphosate degradation);Noncarbon-Nutrients (Inorganic Nutrient Metabolism);PWY-7805 ((aminomethyl)phosphonate degradation);PWY-7807 (glyphosate degradation III);Phosphorus-Compounds (Phosphorus Compound Metabolism)"

I've debated how to organize it, but it's basically MetaCyc|KEGG:Pathway ID (Pathway Name)

samseaver commented 5 years ago

Last commit is because I somehow introduced two pathways columns