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Fix Sodium Cotransport GPRs #655

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merged 7 commits into from
Jul 6, 2023
Merged

Fix Sodium Cotransport GPRs #655

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b05a1a2
fix: removes MAR05310 for being duplicate of MAR06380 with wrong stoi…
Devlin-Moyer Jun 20, 2023
ccdb77f
fix: replaces inaccurate GPRs of MAR06380 and MAR09887 with accurate …
Devlin-Moyer Jun 20, 2023
30b93f6
merge in latest develop branch
Devlin-Moyer Jun 27, 2023
100ce85
fix: add MAR05310 to rxnRetired column for MAR06380 in model/reaction…
Devlin-Moyer Jun 27, 2023
d604989
make MAR06380 reversible
Devlin-Moyer Jul 5, 2023
2d59575
fix: remove MAR09887 and merge annotations into MAR06896
Devlin-Moyer Jul 5, 2023
6d45eb5
fix: merge in latest develop branch
Devlin-Moyer Jul 5, 2023
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2 changes: 2 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -158,6 +158,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR20015" "R02549" "ABUTD;ABUTDm;R_ABUTD;R_ABUTDm" "" "" "" "" "MNXR95191" "" "" "" 0 "RHEA:19105" "" ""
"MAR20014" "R03283" "R_TMABADH;TMABADH" "" "" "" "" "MNXR104876" "" "" "" 0 "RHEA:17985" "" ""
"MAR20052" "" "ALDD21;RE3076X;R_ALDD21;R_RE3076X" "" "" "" "" "MNXR95747" "" "" "" 0 "RHEA:44016" "" ""
"MAR05310" "" "GLNtN1" "" "" "" "GLNtN1" "MNXR100263" "HMR_5310" "RCR41006" "" 0 "" "" "HMR_5310"
"MAR00032" "" "" "" "" "" "HMR_0032" "" "HMR_0032" "RCR14836" "" 0 "" "" "HMR_0032"
"MAR02276" "" "r0993" "" "" "" "r0993" "MNXR105414" "" "" "" 0 "" "" "r0993"
"MAR02277" "" "r0994" "" "" "" "r0994" "MNXR105415" "" "" "" 0 "" "" "r0994"
Expand Down Expand Up @@ -188,3 +189,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR03441" "" "RE3150C" "" "" "" "RE3150C" "MNXR103806" "" "" "" 0 "" "" "RE3150C"
"MAR10164" "" "" "" "" "" "CE2516t" "" "" "" "" 0 "" "" "CE2516t"
"MAR10433" "" "" "" "" "" "EX_CE2516[e]" "" "" "" "" 0 "" "" "EX_CE2516[e]"
"MAR09887" "" "GLNB0AT3tc" "" "" "" "GLNB0AT3tc" "" "" "" "" 0 "" "" "GLNB0AT3tc"
44 changes: 2 additions & 42 deletions model/Human-GEM.yml
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Expand Up @@ -172213,26 +172213,6 @@
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR05310"
- name: ""
- metabolites: !!omap
- MAM01975c: 1
- MAM01975e: -1
- MAM02039c: -1
- MAM02039e: 1
- MAM02519c: 2
- MAM02519e: -2
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000017483 or ENSG00000188338"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: ""
- references: ""
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR05311"
- name: ""
Expand Down Expand Up @@ -188970,9 +188950,9 @@
- MAM02039e: 1
- MAM02519c: 1
- MAM02519e: -1
- lower_bound: 0
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000017483 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209"
- gene_reaction_rule: "ENSG00000017483 or ENSG00000188338"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: ""
Expand Down Expand Up @@ -248845,26 +248825,6 @@
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR09887"
- name: "Glutamine Transport by B0At3"
- metabolites: !!omap
- MAM01442c: 1
- MAM01442e: -1
- MAM01975c: 1
- MAM01975e: -1
- MAM02519c: 1
- MAM02519e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000147003 and ENSG00000164363"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR09888"
- name: "Glutamate Transport by B0At3"
Expand Down
6 changes: 2 additions & 4 deletions model/reactions.tsv
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Expand Up @@ -5397,7 +5397,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR05305" "" "ALAt4" "" "r1118" "" "ALAt4" "MNXR95692" "HMR_5305" "RCR41003" "2.A.18.6.7" 0 "" "" "HMR_5305"
"MAR05307" "" "ALAtN1" "" "" "" "ALAtN1" "MNXR95705" "HMR_5307" "RCR41004" "" 0 "" "" "HMR_5307"
"MAR05308" "" "GLNt4" "" "r1119" "" "GLNt4" "MNXR100261" "HMR_5308" "RCR41005" "2.A.18.6.5" 0 "" "" "HMR_5308"
"MAR05310" "" "GLNtN1" "" "" "" "GLNtN1" "MNXR100263" "HMR_5310" "RCR41006" "" 0 "" "" "HMR_5310"
"MAR05311" "" "ASNt4" "" "r1120" "" "ASNt4" "MNXR96057" "HMR_5311" "RCR41007" "2.A.18.6.7" 0 "" "" "HMR_5311"
"MAR05313" "" "ASNtN1" "" "" "" "ASNtN1" "MNXR96068" "HMR_5313" "RCR41008" "" 0 "" "" "HMR_5313"
"MAR05314" "" "VALt4" "" "r1121" "" "VALt4" "MNXR105189" "HMR_5314" "RCR41009" "2.A.1.44.1" 0 "" "" "HMR_5314"
Expand Down Expand Up @@ -6275,7 +6274,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR06375" "" "SERt4" "" "r2474" "" "SERt4" "MNXR104346" "HMR_6375" "RCR41525" "2.A.18.6.5" 0 "" "" "HMR_6375"
"MAR06377" "" "CYSt4" "" "r2475" "" "CYSt4" "MNXR97028" "HMR_6377" "RCR41526" "2.A.18.6.5" 0 "" "" "HMR_6377"
"MAR06379" "" "HOMt4" "" "r2476" "" "HOMt4" "MNXR100677" "HMR_6379" "RCR41527" "2.A.18.6.5" 0 "" "" "HMR_6379"
"MAR06380" "" "GLNt4" "" "r2477" "" "" "MNXR100261" "HMR_6380" "RCR41528" "2.A.18.6.2" 0 "" "" "HMR_6380"
"MAR06380" "" "GLNt4;GLNtN1" "" "r2477" "" "GLNtN1" "MNXR100261;MNXR100263" "HMR_6380;HMR_5310" "RCR41528;RCR41006" "2.A.18.6.2" 0 "" "" "HMR_6380;HMR_5310;MAR05310"
"MAR06381" "" "SERt4" "" "r2478" "" "" "MNXR104346" "HMR_6381" "RCR41529" "2.A.18.6.8" 0 "" "" "HMR_6381"
"MAR06382" "" "ASNt4" "" "r2479" "" "" "MNXR96057" "HMR_6382" "RCR41530" "2.A.18.6.8" 0 "" "" "HMR_6382"
"MAR06383" "" "HOMt4" "" "r2480" "" "" "MNXR100677" "HMR_6383" "RCR41531" "2.A.18.6.8" 0 "" "" "HMR_6383"
Expand Down Expand Up @@ -9504,7 +9503,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR06891" "" "CYSTALArBATtc" "" "" "" "CYSTALArBATtc" "MNXR97011" "" "" "" 0 "" "" "CYSTALArBATtc"
"MAR06892" "" "CYSTLEUrBATtc" "" "" "" "CYSTLEUrBATtc" "MNXR97016" "" "" "" 0 "" "" "CYSTLEUrBATtc"
"MAR06893" "" "FOLt" "" "" "" "FOLTle" "MNXR99612" "" "" "" 0 "" "" "FOLTle"
"MAR06896" "" "GLNATB0tc" "" "" "" "GLNATB0tc" "MNXR100248" "" "" "" 0 "" "" "GLNATB0tc"
"MAR06896" "" "GLNATB0tc;GLNB0AT3tc" "" "" "" "GLNATB0tc;GLNB0AT3tc" "MNXR100248" "" "" "" 0 "" "" "GLNATB0tc;GLNB0AT3tc;MAR09887"
"MAR06897" "" "GLNyLATthc" "" "" "" "GLNyLATthc" "MNXR100264" "" "" "" 0 "" "" "GLNyLATthc"
"MAR06898" "" "GLYGLYCNc" "" "" "" "GLYGLYCNc" "MNXR100345" "" "" "" 0 "" "" "GLYGLYCNc"
"MAR06899" "" "GLYGLYPEPT1tc" "" "" "" "GLYGLYPEPT1tc" "MNXR100346" "" "" "" 0 "" "" "GLYGLYPEPT1tc"
Expand Down Expand Up @@ -9740,7 +9739,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR09884" "" "FOLOAT2tc" "" "" "" "FOLOAT2tc" "" "" "" "" 0 "" "" "FOLOAT2tc"
"MAR09885" "" "FOLOATPtc" "" "" "" "FOLOATPtc" "" "" "" "" 0 "" "" "FOLOATPtc"
"MAR09886" "" "GABABGTtc" "" "" "" "GABABGTtc" "" "" "" "" 0 "" "" "GABABGTtc"
"MAR09887" "" "GLNB0AT3tc" "" "" "" "GLNB0AT3tc" "" "" "" "" 0 "" "" "GLNB0AT3tc"
"MAR09888" "" "GLUB0AT3tc" "" "" "" "GLUB0AT3tc" "" "" "" "" 0 "" "" "GLUB0AT3tc"
"MAR09889" "" "GSNt2" "" "" "" "GSNt2r" "MNXR100434" "" "" "" 0 "RHEA:29586" "RHEA:29583" "GSNt2r"
"MAR09890" "" "H2OGLYAQPt" "" "" "" "H2OGLYAQPt" "" "" "" "" 0 "" "" "H2OGLYAQPt"
Expand Down