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Remove Tagatose-1,6-Bisphosphate #807

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merged 5 commits into from
Apr 24, 2024
Merged

Remove Tagatose-1,6-Bisphosphate #807

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92d5295
fix: removed MAR04774, MAR04775, and MAM02955c from YAML file
Devlin-Moyer Feb 23, 2024
e4849bd
chore: moved row for MAM02955c from model/metabolites.tsv to data/dep…
Devlin-Moyer Feb 23, 2024
235a087
chore: moved rows for MAR04774 and MAR04775 from model/reactions.tsv …
Devlin-Moyer Feb 23, 2024
b4711dd
feat: added references for tagatose metabolism reactions
Devlin-Moyer Feb 23, 2024
3a16284
chore: resolve merge conflicts with latest version of develop branch
Devlin-Moyer Apr 23, 2024
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1 change: 1 addition & 0 deletions data/deprecatedIdentifiers/deprecatedMetabolites.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -2271,3 +2271,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM03203m" "MAM03203" "3ddecdicoa" "" "" "" "5280771" "" "" "" "3ddecdicoa" "" "" "3ddecdicoa_m"
"MAM02698m" "MAM02698" "2ddecdicoa" "" "" "" "5280770" "" "" "" "2ddecdicoa" "" "" "2ddecdicoa_m"
"MAM03650m" "MAM03650" "hexddcoa" "" "" "" "" "" "" "" "hexddcoa" "" "" "hexddcoa_m"
"MAM02955c" "MAM02955" "" "C03785" "" "CHEBI:4250" "440117" "" "" "HC01180" "HC01180" "MNXM1324;MNXM164715" "m02955c" "m02955c"
2 changes: 2 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -295,3 +295,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR05075" "" "FAOXC122m" "" "" "" "FAOXC122m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC122m;HMR_3422;MAR03422"
"MAR05072" "" "FAOXC122C101m" "" "" "" "FAOXC122C101m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC122C101m;HMR_3422;MAR03422"
"MAR00965" "" "FAOXC2252053m" "" "" "" "FAOXC2252053m" "MNXR99352" "" "" "" 0 "" "" "FAOXC2252053m"
"MAR04774" "R03237" "" "R03237C" "r0610" "" "r0610" "MNXR105355;MNXR108039" "HMR_4774" "RCR11046" "" 0 "" "" "HMR_4774"
"MAR04775" "R03239" "" "R03239C" "r0611" "" "r0611" "MNXR105356;MNXR108041" "HMR_4775" "RCR14197" "" 0 "" "" "HMR_4775"
58 changes: 6 additions & 52 deletions model/Human-GEM.yml
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Expand Up @@ -40793,14 +40793,6 @@
- charge: 0
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02955c"
- name: "tagatose-1,6-bisphosphate"
- compartment: "c"
- formula: "C6H10O12P2"
- charge: -4
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02956e"
- name: "TAG-chylomicron pool"
Expand Down Expand Up @@ -68998,44 +68990,6 @@
- subsystem:
- "Galactose metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04774"
- name: "CTP:D-tagatose 6-phosphate 1-phosphotransferase"
- metabolites: !!omap
- MAM01424c: -1
- MAM01623c: 1
- MAM01746c: 1
- MAM02039c: -1
- MAM02955c: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000067057 or ENSG00000141959 or ENSG00000152556"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.1.11"
- references: "PMID:131802;PMID:1810251;PMID:193556;PMID:2987258;PMID:6091737"
- subsystem:
- "Galactose metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04775"
- name: "ITP:D-tagatose 6-phosphate 1-phosphotransferase"
- metabolites: !!omap
- MAM01746c: -1
- MAM02039c: 1
- MAM02161c: 1
- MAM02193c: -1
- MAM02955c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000067057 or ENSG00000141959 or ENSG00000152556"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.1.11"
- references: "PMID:131802;PMID:1810251"
- subsystem:
- "Galactose metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04831"
- name: "Lactose:(acceptor) 3-oxidoreductase"
Expand Down Expand Up @@ -69107,7 +69061,7 @@
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.1.3"
- references: ""
- references: "PMID:33715524"
- subsystem:
- "Galactose metabolism"
- confidence_score: 0
Expand All @@ -69124,7 +69078,7 @@
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "4.1.2.13"
- references: ""
- references: "PMID:33715524"
- subsystem:
- "Galactose metabolism"
- confidence_score: 0
Expand Down Expand Up @@ -191976,7 +191930,7 @@
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: ""
- references: ""
- references: "PMID:33715524"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand Down Expand Up @@ -215766,7 +215720,7 @@
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: ""
- references: ""
- references: "PMID:33715524"
- subsystem:
- "Exchange/demand reactions"
- confidence_score: 0
Expand Down Expand Up @@ -222350,7 +222304,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "4.1.2.13"
- references: "PMID:2996495;PMID:6284103;PMID:6298387"
- references: "PMID:33715524"
- subsystem:
- "Galactose metabolism"
- confidence_score: 0
Expand Down Expand Up @@ -223360,7 +223314,7 @@
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "2.7.1.3"
- references: "PMID:2996495;PMID:6284103;PMID:6298387"
- references: "PMID:33715524"
- subsystem:
- "Galactose metabolism"
- confidence_score: 0
Expand Down
1 change: 0 additions & 1 deletion model/metabolites.tsv
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Expand Up @@ -5097,7 +5097,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02952e" "MAM02952" "" "C03642" "" "CHEBI:17864" "440071" "LMST05020003" "" "HC02198" "HC02198" "MNXM162796;MNXM1950" "m02952s" "m02952s"
"MAM02953c" "MAM02953" "ts3" "" "HMDB0006560" "" "5283713" "" "" "" "ts3" "MNXM21968" "m02953c" "m02953c"
"MAM02954c" "MAM02954" "" "C11148" "" "CHEBI:28888" "" "" "" "" "M02954" "MNXM3722" "m02954c" "m02954c"
"MAM02955c" "MAM02955" "" "C03785" "" "CHEBI:4250" "440117" "" "" "HC01180" "HC01180" "MNXM1324;MNXM164715" "m02955c" "m02955c"
"MAM02956e" "MAM02956" "" "C00422" "" "CHEBI:17855" "" "LMGL03010000" "" "" "M02956" "MNXM248" "m02956s" "m02956s"
"MAM02957e" "MAM02957" "" "C00422" "" "CHEBI:17855" "" "LMGL03010000" "" "" "M02957" "MNXM248" "m02957s" "m02957s"
"MAM02958c" "MAM02958" "" "C00422" "" "CHEBI:17855" "" "LMGL03010000" "" "" "M02958" "MNXM248" "m02958c" "m02958c"
Expand Down
2 changes: 0 additions & 2 deletions model/reactions.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -76,8 +76,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR04414" "R01092" "" "R01092C" "r0265" "" "GALK" "MNXR99985" "HMR_4414" "RCR10454" "" 0 "" "RHEA:13553" "HMR_4414"
"MAR04415" "R01100" "LACZe" "R01100C" "r0266" "" "LACZe" "MNXR101000" "HMR_4415" "RCR30497" "" 0 "" "RHEA:10076" "HMR_4415"
"MAR04416" "R01104" "" "R01104C" "r0627" "" "r0627" "MNXR100115" "HMR_4416" "RCR30257" "" 0 "" "" "HMR_4416"
"MAR04774" "R03237" "" "R03237C" "r0610" "" "r0610" "MNXR105355;MNXR108039" "HMR_4774" "RCR11046" "" 0 "" "" "HMR_4774"
"MAR04775" "R03239" "" "R03239C" "r0611" "" "r0611" "MNXR105356;MNXR108041" "HMR_4775" "RCR14197" "" 0 "" "" "HMR_4775"
"MAR04831" "R01680" "" "" "" "" "HMR_4831" "MNXR107115" "HMR_4831" "RCR30498" "" 0 "" "" "HMR_4831"
"MAR04832" "R04783" "" "R04783C" "r0737" "" "r0737" "MNXR105374;MNXR109113" "HMR_4832" "RCR30499" "" 0 "" "" "HMR_4832"
"MAR07674" "R00503" "UGALGTg" "" "" "" "UGALGTg" "MNXR105080" "HMR_7674" "RCR11047" "" 0 "" "RHEA:12404" "HMR_7674"
Expand Down
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