Remove Mitochondrial Bile Acid Synthesis Pathway #669
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…nto MAR01642 and MAR01646
Devlin-Moyer
changed the title
| "MAR01653" "R03719" "SCPx" "R03719X" "r0628" "" "HMR_1653" "MNXR104297;MNXR108369" "HMR_1653" "RCR13610" "" 0 "" "RHEA:16865" "HMR_1653" | ||
| "MAR01656" "" "" "" "r0990" "" "r0990" "MNXR105412" "HMR_1656" "RCR20134" "" 0 "" "" "HMR_1656" | ||
| "MAR01659" "" "" "" "r2501" "" "r2501" "MNXR106313" "HMR_1659" "RCR20234" "3.A.1.203.3" 0 "" "" "HMR_1659" | ||
| "MAR01632" "R08734" "" "RE2624X" "" "R-HSA-192056" "AMACRp;RE2624X;HMR_1635;RE2624M" "MNXR112240" "HMR_1632;HMR_1635" "RCR10915;RCR13606" "" 0 "RHEA:40456" "RHEA:40455" "HMR_1632;HMR_1635;MAR01635" |
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@haowang-bioinfo Is the last column correct? Shouldn't rxnRetired refer to reaction identifiers for the exact same reaction? Because rxnRetired here also includes MARxxxxx identifiers of similar reactions that were deleted. For instance, MAR01632 is the peroxisome variant that is kept, while MAR01635. In the current file MAR01635 is added as rxnRetired for MAR01632, but I don't think that's correct?
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Shouldn't rxnRetired refer to reaction identifiers for the exact same reaction?
good question, and yes the ones in rxnRetired should be the reactions that are the same or similar to that represented by master id
In the current file MAR01635 is added as rxnRetired for MAR01632, but I don't think that's correct?
agree, adding MAR01635 as rxnRetired for MAR01632 is incorrect. Because they are in different compartments therefore not duplicate to each other
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ah okay I was thinking of MAR01635 as the (wrongly) mitochondrial "duplicate" of MAR01632; I can undo that
I also added the IDs from other models that were associated with MAR01635 to the lists of IDs associated with MAR01632; should I also undo that? I figured that might be helpful if you were wondering why the mitochondrial version of the reaction in, say, Recon3D doesn't appear to be in Human-GEM, and seeing it in the row for MAR01632 might convey that it was dropped because the peroxisomal version was the only "correct" one? No idea if that would actually be clear to a hypothetical future observer though, and could just be extra confusing for no reason
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No idea if that would actually be clear to a hypothetical future observer though, and could just be extra confusing for no reason
everything should be clear to future observers given the provided messages in this PR
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@Devlin-Moyer great work! will give a thorough check asap |
Main improvements in this PR:
As proposed in #637:
MAR01630for being implausible mitochondrial version of peroxisomalMAR01629MAR01635for being implausible mitochondrial version of peroxisomalMAR01632MAR01637for being implausible mitochondrial version of peroxisomalMAR01639andMAR01638MAR01644for being implausible mitochondrial version of peroxisomalMAR01642MAR01651for being implausible mitochondrial version of peroxisomalMAR01646MAR01653for being implausible mitochondrial version of peroxisomalMAR01652MAR03754for being implausible mitochondrial version of peroxisomalMAR03756MAR03760for being implausible mitochondrial version of peroxisomalMAR03764MAR01662for being implausible mitochondrial version of peroxisomalMAR01663MAR01666for being implausible mitochondrial version of peroxisomalMAR01665MAR01656for being incorrectly ATP-independent version of ATP-dependentMAR01659MAR07758since there’s no evidence of transport of cholyl-CoA into mitochondriaMAR01458for being redundant withMAR01642+MAR01646MAM00616m,MAM00618m,MAM00749m,MAM00036m,MAM00748m,MAM03367m,MAM01445m, andMAM01514m(I missed some of these when making the original list in Duplicate Bile Acid Synthesis Reactions #637 but the YAML validation check pointed them out, so I updated the list here and in Duplicate Bile Acid Synthesis Reactions #637)I hereby confirm that I have:
developas a target branch