search

SysBioChalmers / Human-GEM

The generic genome-scale metabolic model of Homo sapiens
https://sysbiochalmers.github.io/Human-GEM-guide/
Creative Commons Attribution 4.0 International
97 stars 40 forks source link

A metabolite appears on both sides of an equation #308

Closed mpagni12 closed 2 years ago

mpagni12 commented 3 years ago

Description of the issue:

A metabolite or its xrefs should NOT appear on both sides of an equation

For example, in reaction MAR04499:

1 MAM02039@m + 1 MAM02485@m + 1 MAM02741@m <?> 1 MAM02040@m + 1 MAM02484@m

the following xrefs are given:

 MAM02484   kegg:C03688;lipidmaps:PROTEIN;mnx:MNXM91491;vmhmetabolite:HC02223
 MAM02485   kegg:C03688;lipidmaps:PROTEIN;mnx:MNXM91491;vmhmetabolite:HC02222

i.e. MAM02484 and MAM02485 is the same metabolite!

Marco

Two other equations are affected by the same problem: MAR09464 and MAR9487

I hereby confirm that I have:

haowang-bioinfo commented 3 years ago

@mpagni12 thanks! how do you suggest to fix this?

mpagni12 commented 3 years ago

Rewrite the equation using explicitly the ACP-x and ACP-y metabolites from ChEBI. See

https://www.rhea-db.org/rhea?query=ACP

for an already long list of reactions with similar pattern. Maybe your three equations are already in this list?

haowang-bioinfo commented 3 years ago

it seems the annotation to MAM02484 was wrong, should be revised.

haowang-bioinfo commented 3 years ago

  1. MAR04499: according to the KEGG (R01623) and Rhea (20540) annotation, MAM02484 should be annotated as CHEBI:64479, while MAM02485 as CHEBI:29999.

  2. MAR09464: this is actually a hydrolysis reaction that has dextrin polymer on both sides, the product has one less monomer (glucose) than reactant.

  3. MAR09487: similar to MAR09464, MAR09487 also has polymers on both sides.

@mpagni12 what do you suggest to deal with polymerization reacton?

mihai-sysbio commented 2 years ago

Has already been solved as part of the merged PR?

haowang-bioinfo commented 2 years ago

no

mihai-sysbio commented 2 years ago

Since MAR09464 and MAR9487 are polymerization reactions, there doesn't seem to be an obvious solution to these.

If desired, please open up an issue generically targeting polymerization reactions, giving the examples of MAR09464 and MAR9487 and linking to this thread. With this, I am considering the issue of having the same metabolite on both sides of the equation resolved.