fix: miscellaneous curations #325
Conversation
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@smoretti the met ids haven't been fixed, but will do this |
- revert compartment change from p to x, will revisit this after thorough planning
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@smoretti the changes of compartment abbreviation and met ids will be made elsewhere, due to some new discussions in #314 @ANiknejad could you please review the changes in this PR |
| @@ -4618,8 +4618,8 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa | |||
| "MAM02678m" "MAM02678" "pmtcoa" "C00154" "HMDB01338" "CHEBI:15525" "15667" "LMFA07050002" "" "HC00150" "pmtcoa" "MNXM88" "m02678m" "m02678m" | |||
| "MAM02678p" "MAM02678" "pmtcoa" "C00154" "HMDB01338" "CHEBI:15525" "15667" "LMFA07050002" "" "HC00150" "pmtcoa" "MNXM88" "m02678p" "m02678p" | |||
| "MAM02678r" "MAM02678" "pmtcoa" "C00154" "HMDB01338" "CHEBI:15525" "15667" "LMFA07050002" "" "HC00150" "pmtcoa" "MNXM88" "m02678r" "m02678r" | |||
| "MAM02679c" "MAM02679" "ptth" "C00154" "HMDB01338" "CHEBI:15525" "15667" "" "" "HC00554" "ptth" "MNXM1154" "m02679c" "m02679c" | |||
| "MAM02679m" "MAM02679" "ptth" "C00154" "HMDB01338" "CHEBI:15525" "15667" "" "" "HC00554" "ptth" "MNXM1154" "m02679m" "m02679m" | |||
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Why was the associated metBiGGID ptth removed? I think that association was correct.
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yes, ptth does appear to be correctly annotated in BiGG.
This removal was due to the wrong annotation to metRecon3DID id ptth, which probably should be removed?
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Ah, very interesting case - so the ptth entry is correct in BiGG but incorrect in VMH. Although I would like to maintain the association with the Recon3D ID, it may be better to remove it to avoid confusion...
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Yes, it is.
Now the BiGG id was added back, while the erroneous Recon3D id excluded.
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@smoretti if this PR can be merged without dealing with compartment abbreviation, which obviously needs more thoughts |
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I think it can be merged without the compartment abbreviation change |
Main improvements in this PR:
change Perxisome compartment abbreviation fromptox, as discussed in Why all compartment ids are not consistent? #314MAM02484andMAM02485as reported in A metabolite appears on both sides of an equation #308MAM00003,MAM00005, andMAM00046as suggested in adding chebi as a xref to MAM00003(c) #299, list of MAMids that can have new chebi xref #300I hereby confirm that I have:
developas a target branch