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fix-remove the duplicate met MAM00077x and corresponding rxns #534

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merged 3 commits into from
Apr 14, 2023
Merged

fix-remove the duplicate met MAM00077x and corresponding rxns #534

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e629d36
fix-remove the duplicate mets and corresponding rxns
feiranl Apr 14, 2023
ffeca7f
fix-met: move GPR from MAR03488 to MAR03386
haowang-bioinfo Apr 14, 2023
e7a8f78
Merge remote-tracking branch 'origin/develop' into rm-duplicate
haowang-bioinfo Apr 14, 2023
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1 change: 1 addition & 0 deletions data/deprecatedIdentifiers/deprecatedMetabolites.tsv
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Expand Up @@ -2190,3 +2190,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM00890l" "MAM00890" "3ohodcoa" "C16216" "HMDB06498" "CHEBI:50571" "22833663" "" "" "" "3ohodcoa" "MNXM513" "" "m00890l"
"MAM00156c" "MAM00156" "" "" "" "" "53481438" "" "CE2196" "" "CE2196" "MNXM31535" "m00156c" "m00156c"
"MAM02045c" "MAM02045" "" "C09209" "" "CHEBI:5623" "5281404" "" "" "" "C09209" "MNXM11747" "m02045c" "m02045c"
"MAM00077x" "MAM00077" "CE2416" "" "" "" "" "" "CE2416" "" "" "MNXM165274" "m00077p" "m00077p"
2 changes: 2 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -70,3 +70,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR04586" "R01899" "" "R01899C" "r0423" "" "r0423" "MNXR105340" "HMR_4586" "RCR11668" "" 0 "" "RHEA:25588" "HMR_4586"
"MAR04587" "R01899" "" "R01899C" "r0424" "" "r0424" "MNXR105340" "HMR_4587" "RCR10604" "" 0 "" "RHEA:25588" "HMR_4587"
"MAR04588" "" "" "" "r0425" "" "r0425" "MNXR105341" "HMR_4588" "RCR11669" "" 0 "" "" "HMR_4588"
"MAR03488" "" "" "RE3073X" "" "" "" "MNXR95747" "HMR_3488" "RCR12589" "" 0 "" "" "HMR_3488"
"MAR03489" "" "" "RE3079X" "" "" "" "" "HMR_3489" "RCR12590" "" 0 "" "" "HMR_3489"
54 changes: 3 additions & 51 deletions model/Human-GEM.yml
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Expand Up @@ -4,7 +4,7 @@
short_name: "Human-GEM"
full_name: "Generic genome-scale metabolic model of Homo sapiens"
version: ""
date: "2023-03-29"
date: "2023-04-14"
authors: "Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas"
email: "jonrob@chalmers.se"
organization: "Chalmers University of Technology"
Expand Down Expand Up @@ -1188,14 +1188,6 @@
- charge: -4
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00077x"
- name: "(2R,6S,10S)-pristanate"
- compartment: "x"
- formula: "C19H37O2"
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00078x"
- name: "(2S)-pristanoyl-CoA"
Expand Down Expand Up @@ -117714,46 +117706,6 @@
- subsystem:
- "Beta oxidation of phytanic acid (peroxisomal)"
- confidence_score: 0
- !!omap
- id: "MAR03488"
- name: ""
- metabolites: !!omap
- MAM00077x: 1
- MAM00564x: -1
- MAM02039x: 2
- MAM02040x: -1
- MAM02552x: -1
- MAM02553x: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000107537"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.14.11.18"
- references: "PMID:9662422;PMID:9662422;PMID:11356164;PMID:11356164"
- subsystem:
- "Beta oxidation of phytanic acid (peroxisomal)"
- confidence_score: 0
- !!omap
- id: "MAR03489"
- name: ""
- metabolites: !!omap
- MAM00077x: -1
- MAM00078x: 1
- MAM01334x: 1
- MAM01371x: -1
- MAM01597x: -1
- MAM02759x: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000068366 or ENSG00000103740 or ENSG00000119673 or ENSG00000123983 or ENSG00000130377 or ENSG00000140284 or ENSG00000151726 or ENSG00000164398 or ENSG00000177465 or ENSG00000197142"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "6.2.1.3"
- references: "PMID:11356164;PMID:11356164"
- subsystem:
- "Beta oxidation of phytanic acid (peroxisomal)"
- confidence_score: 0
- !!omap
- id: "MAR03491"
- name: ""
Expand Down Expand Up @@ -234250,7 +234202,7 @@
- MAM02766x: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- gene_reaction_rule: "ENSG00000107537"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "1.2.1.48"
Expand All @@ -234270,7 +234222,7 @@
- MAM02766x: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000068366 or ENSG00000123983 or ENSG00000140284 or ENSG00000151726 or ENSG00000164398 or ENSG00000197142"
- gene_reaction_rule: "ENSG00000068366 or ENSG00000103740 or ENSG00000119673 or ENSG00000123983 or ENSG00000130377 or ENSG00000140284 or ENSG00000151726 or ENSG00000164398 or ENSG00000177465 or ENSG00000197142"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "6.2.1.3"
Expand Down
1 change: 0 additions & 1 deletion model/metabolites.tsv
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Expand Up @@ -146,7 +146,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM00074c" "MAM00074" "" "" "" "" "" "" "CE4835" "" "CE4835" "MNXM145822" "m00074c" "m00074c"
"MAM00075x" "MAM00075" "" "" "" "CHEBI:20067" "" "LMFA07050065" "CE5126" "" "CE5126" "MNXM108213;MNXM35866" "m00075p" "m00075p"
"MAM00076x" "MAM00076" "" "" "" "" "" "" "CE5936" "" "CE5936" "" "m00076p" "m00076p"
"MAM00077x" "MAM00077" "CE2416" "" "" "" "" "" "CE2416" "" "" "MNXM165274" "m00077p" "m00077p"
"MAM00078x" "MAM00078" "pristcoa" "" "" "CHEBI:64039" "" "LMFA07050064" "CE5125" "" "CE5125" "MNXM30947" "m00078p" "m00078p"
"MAM00079x" "MAM00079" "" "" "" "" "53481417" "" "CE5941" "" "CE5941" "MNXM30996" "m00079p" "m00079p"
"MAM00080x" "MAM00080" "" "" "" "" "53481419" "" "CE5935" "" "CE5935" "MNXM30997" "m00080p" "m00080p"
Expand Down
2 changes: 0 additions & 2 deletions model/reactions.tsv
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Expand Up @@ -2625,8 +2625,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR03482" "R03631" "" "RE3075X" "" "R-HSA-389622" "" "MNXR108311" "HMR_3482" "RCR12586" "" 0 "" "RHEA:21380" "HMR_3482"
"MAR03484" "R05722" "" "RE3066X" "" "R-HSA-389639" "PHYHx" "MNXR109782" "HMR_3484" "RCR12587" "" 0 "" "RHEA:16065" "HMR_3484"
"MAR03486" "" "" "RE3072X" "" "R-HSA-389611" "HPCLx" "MNXR118525" "HMR_3486" "RCR12588" "" 0 "RHEA:25356" "RHEA:25355" "HMR_3486"
"MAR03488" "" "" "RE3073X" "" "" "" "MNXR95747" "HMR_3488" "RCR12589" "" 0 "" "" "HMR_3488"
"MAR03489" "" "" "RE3079X" "" "" "" "" "HMR_3489" "RCR12590" "" 0 "" "" "HMR_3489"
"MAR03491" "" "" "RE2759X" "" "R-HSA-389897" "HMR_3491;RE2759X" "MNXR124916" "HMR_3491" "RCR12591" "" 0 "RHEA:40450" "RHEA:40447" "HMR_3491"
"MAR03493" "" "" "RE3079C" "" "R-HSA-389632" "RE3079X" "MNXR103786;MNXR123753" "HMR_3493" "RCR12592" "" 0 "RHEA:47265" "RHEA:47264" "HMR_3493"
"MAR03498" "" "" "RE3086X" "" "R-HSA-389889" "RE3086X" "MNXR124340" "HMR_3498" "RCR12593" "" 0 "RHEA:40460" "RHEA:40459" "HMR_3498"
Expand Down