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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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Place-marker for MetaCyc reaction RXN-1623 (rxn37218) #9

Open samseaver opened 9 years ago

samseaver commented 9 years ago

Firstly, I'm not going to attempt to fix this reaction directly right now, though I've now come to understand what happened, as it's only available in the plant template.

This reaction was brought to my attention because it's the last of the reactions in the ModelTemplate which was previously balanced, and is now mass-imbalanced. It's one of the reactions in a BioCyc database where I attempted to "expand" from the generic compound classes into a series of balanced reactions with individual compounds that have a defined structure (and successfully so in many cases).

But what happened in this particular case is that the compounds in question, being the most commonly addressed in metabolism (for want of a better phrase, i.e. 1-oleyl-2-lyso-phosphatidate is one of the most common components of the cellular membrane) were also assigned the generic names, such as L-1-lysophosphatidate, and thus somehow being merged with the generic compounds with no defined structure.

My problem really is that the compound that is represented here:

http://metacyc.org/META/NEW-IMAGE?type=NIL&object=L-1-LYSOPHOSPHATIDATE

has been completely subsumed somehow, and I'll have to add a whole new compound object back into the compounds list.

samseaver commented 9 years ago

Bad reactions associated to this problem were removed: https://github.com/ModelSEED/ModelSEEDDatabase/commit/51ea51c06da50e9deae0e074ed1f3bcde225d905

JamesJeffryes commented 7 years ago

Can we close this @samseaver?

samseaver commented 7 years ago

No I never got round to truly fixing this. The outcome of this problem was that a single instance of bad integration between two public databases led to a set of imbalanced reactions that could not be used. I need to re-review the impact of this, I can't remember.