diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index ffd2c7f7..475f3701 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -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" diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index e92d5aae..35aeae28 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -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" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 96718b3b..6b729f37 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -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" @@ -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" @@ -69107,7 +69061,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.3" - - references: "" + - references: "PMID:33715524" - subsystem: - "Galactose metabolism" - confidence_score: 0 @@ -69124,7 +69078,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.1.2.13" - - references: "" + - references: "PMID:33715524" - subsystem: - "Galactose metabolism" - confidence_score: 0 @@ -191976,7 +191930,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "" + - references: "PMID:33715524" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -215766,7 +215720,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "" + - references: "PMID:33715524" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -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 @@ -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 diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 7c6f6277..cf78e5a6 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -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" diff --git a/model/reactions.tsv b/model/reactions.tsv index 01d8a9bd..69a19d93 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -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"