From 92d52957c15181323b34097586fe923eb469596a Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 23 Feb 2024 09:29:47 -0500 Subject: [PATCH 1/4] fix: removed MAR04774, MAR04775, and MAM02955c from YAML file --- model/Human-GEM.yml | 46 --------------------------------------------- 1 file changed, 46 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 5db5b246..ae997a3e 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" @@ -69062,44 +69054,6 @@ - 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" From e4849bd04da7b2552949c2ba2af6b84faf74b344 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 23 Feb 2024 09:31:01 -0500 Subject: [PATCH 2/4] chore: moved row for MAM02955c from model/metabolites.tsv to data/deprecatedIdentifiers/deprecatedMetabolties.tsv --- data/deprecatedIdentifiers/deprecatedMetabolites.tsv | 1 + model/metabolites.tsv | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index d935bba1..f9bff2b0 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2263,3 +2263,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02158n" "MAM02158" "" "" "" "" "124985" "" "CE2011" "" "CE2011" "MNXM57006" "" "m02158n" "MAM00678c" "MAM00678" "" "" "" "" "22833562" "" "CE2435" "" "dec24dicoa" "MNXM1601" "" "m00678c" "MAM03035c" "MAM03035" "" "" "" "" "16019966" "" "CE5121" "" "dece3coa" "MNXM90096" "" "m03035c" +"MAM02955c" "MAM02955" "" "C03785" "" "CHEBI:4250" "440117" "" "" "HC01180" "HC01180" "MNXM1324;MNXM164715" "m02955c" "m02955c" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index b3ed31cc..76d73398 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" From 235a087fad9afeb4d18098dd2cf98d939062ab14 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 23 Feb 2024 09:32:03 -0500 Subject: [PATCH 3/4] chore: moved rows for MAR04774 and MAR04775 from model/reactions.tsv to data/deprecatedIdentifiers/deprecatedReactions.tsv --- data/deprecatedIdentifiers/deprecatedReactions.tsv | 2 ++ model/reactions.tsv | 2 -- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index c21654f1..9fc51b05 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -283,3 +283,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03296" "" "" "RE3627M" "" "R-HSA-109343" "HMR_3296" "MNXR124610" "HMR_3296" "RCR12779" "" 0 "" "" "HMR_3296" "MAR04005" "" "" "" "" "" "RE3627C" "" "" "" "" 0 "" "" "RE3627C" "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/reactions.tsv b/model/reactions.tsv index 942c434f..db098e26 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" From b4711dd55fff1b3aa7357e77360644968914e00e Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 23 Feb 2024 09:33:56 -0500 Subject: [PATCH 4/4] feat: added references for tagatose metabolism reactions --- model/Human-GEM.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index ae997a3e..749bb256 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -69125,7 +69125,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.3" - - references: "" + - references: "PMID:33715524" - subsystem: - "Galactose metabolism" - confidence_score: 0 @@ -69142,7 +69142,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.1.2.13" - - references: "" + - references: "PMID:33715524" - subsystem: - "Galactose metabolism" - confidence_score: 0 @@ -191994,7 +191994,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "" + - references: "PMID:33715524" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -215784,7 +215784,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "" + - references: "PMID:33715524" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -222368,7 +222368,7 @@ - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "4.1.2.13" - - references: "PMID:2996495;PMID:6284103;PMID:6298387" + - references: "PMID:33715524" - subsystem: - "Galactose metabolism" - confidence_score: 0 @@ -223378,7 +223378,7 @@ - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "2.7.1.3" - - references: "PMID:2996495;PMID:6284103;PMID:6298387" + - references: "PMID:33715524" - subsystem: - "Galactose metabolism" - confidence_score: 0