Mouse 1.1 #7
Mouse 1.1 #7
Conversation
style: align with `standard-GEM` template v0.5
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With the versioning in Human-GEM and Mouse-GEM being different, I'm wondering how to make it more obvious to the community what version of the Human-GEM is used. Perhaps the version could be added to the |
| @@ -9,3 +9,4 @@ rxns equations ub lb eccodes subSystems grRules rxnReferences rxnConfidenceScore | |||
| "MA_20008" "O2[r] + L-gulono-1,4-lactone[r] => H2O2[r] + ascorbate[r] + H+[r]" 1000 0 "1.1.3.8" "Ascorbate and aldarate metabolism" "Gulo" "PMID:14962674" 4 "R10053" "RXN-13689" "" "MNXR116004" | |||
| "MA_20009" "O2[r] + L-gulono-1,4-lactone[r] => H2O2[r] + L-xylo-Hexulonolactone[r]" 1000 0 "1.1.3.8" "Ascorbate and aldarate metabolism" "Gulo" "" 2 "R03184" "L-GULONOLACTONE-OXIDASE-RXN" "" "MNXR140097" | |||
| "MA_20010" "PAPS[c] + aniline[c] => PAP[c] + Benzenamine sulfate[c] + H+[c]" 1000 0 "2.8.2.3" "Amine sulfotransferase" "Sult3a1" "" 2 "R01861" "" "" "MNXR107208" | |||
| "MA_20016" "ascorbate[r] => ascorbate[c]" 1000 0 "" "Transport" "" "" 0 "" "" "" "" | |||
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I'm surprised to see this transport reaction as being species-specific. However, it doesn't have any other external identifiers, and no literature reference. Perhaps then it is the result of gap-filling? And if so, shouldn't this reaction be part of Human-GEM - ie, is it really species specific?
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yes, this addition can be viewed as a result of gap-filling for achieving the metabolic task #257 (Biosynthesis of Vitamin C) defined in metabolicTasks_Full.xlsx. And it's not part of Human-GEM, since it's species-specific.
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Seems like this reaction should be reversible, but I realize that's something that should probably be addressed in Human-GEM where it originates.
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This transportation from ER to cytosol is added for modelling purpose. If there is any reference reporting this transporter and indicating the reversibility? @JonathanRob
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Ah, sorry, I didn't realize that these were mouse-specific reactions, not those coming from Human-GEM (even with the painfully obvious file name mouseSpecificRxns.tsv...). I don't know of any specific references, but this paper is probably a good place to start. For now though I think it's fine to keep the gap-filled reaction as you have it.
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Good question. The version dependency information is stored in the dependencies.txt file under |
It looks like that file duplicates some of the dependencies listed in the Readme. According to the DRY principle, I find it better to have only one place to store this. And for ease of access, the |
The |
Main improvements in this PR:
standard-GEMtemplate v0.5 #6):.standard-GEM.mdfile according to the spec ofstandard-GEMver 0.5