From ebc49344263ba874df197b0ca6adf456442edbee Mon Sep 17 00:00:00 2001 From: Jonathan Robinson Date: Wed, 16 Nov 2022 08:54:07 +0100 Subject: [PATCH 1/3] fix: remove reaction MAR02517 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 20 ------------------- model/reactions.tsv | 1 - 3 files changed, 1 insertion(+), 21 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 9fdc2945..da388ff0 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -59,3 +59,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR06857" "" "TETDECE1CRNe" "" "" "" "TETDECE1CRNe" "" "" "" "" 0 "" "" "TETDECE1CRNe" "MAR06858" "" "TIGCRNe" "" "" "" "TIGCRNe" "MNXR104864" "" "" "" 0 "" "" "TIGCRNe" "MAR07191" "" "PNTOte" "" "" "" "PNTORDe" "MNXR103051" "" "" "" 0 "" "" "PNTORDe" +"MAR02517" "" "RE0580L" "" "" "" "RE0580L" "MNXR94939" "" "" "" 0 "" "" "RE0580L" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 607f8b86..9433d243 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -231044,26 +231044,6 @@ - subsystem: - "Fatty acid biosynthesis" - confidence_score: 0 - - !!omap - - id: "MAR02517" - - name: "" - - metabolites: !!omap - - MAM00890l: 1 - - MAM01596l: 1 - - MAM01597l: 1 - - MAM02039l: -1 - - MAM02444l: -1 - - MAM02678l: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000064601" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "3.1.2.2" - - references: "PMID:10479480" - - subsystem: - - "Fatty acid biosynthesis" - - confidence_score: 0 - !!omap - id: "MAR02519" - name: "" diff --git a/model/reactions.tsv b/model/reactions.tsv index e72c5207..4ae9c498 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -8803,7 +8803,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR02506" "" "RE0578X" "" "" "" "RE0578X" "MNXR103463" "" "" "" 0 "" "" "RE0578X" "MAR02507" "" "RE0579M" "" "" "" "RE0579M" "MNXR103464" "" "" "" 0 "" "" "RE0579M" "MAR02508" "" "RE0579X" "" "" "" "RE0579X" "MNXR103464" "" "" "" 0 "" "" "RE0579X" -"MAR02517" "" "RE0580L" "" "" "" "RE0580L" "MNXR94939" "" "" "" 0 "" "" "RE0580L" "MAR02519" "" "RE0580R" "" "" "" "RE0580R" "MNXR94939" "" "" "" 0 "" "" "RE0580R" "MAR02521" "" "RE0581R" "" "" "" "RE0581R" "MNXR103465" "" "" "" 0 "RHEA:35302" "RHEA:35299" "RE0581R" "MAR02523" "" "RE0582N" "" "" "" "RE0582N" "MNXR103466" "" "" "" 0 "RHEA:35350" "RHEA:35347" "RE0582N" From cb3f31e1d475ee5d3ebe1a16dad128bc99ee4532 Mon Sep 17 00:00:00 2001 From: Jonathan Robinson Date: Wed, 16 Nov 2022 08:56:08 +0100 Subject: [PATCH 2/3] fix: correct ec-code for reaction MAR02519 --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 9433d243..d2f08afc 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -231059,7 +231059,7 @@ - gene_reaction_rule: "ENSG00000012660 or ENSG00000066322 or ENSG00000170522 or ENSG00000197977" - rxnNotes: "" - rxnFrom: "Recon3D" - - eccodes: "3.1.2.2" + - eccodes: "2.3.1.199" - references: "PMID:10479480" - subsystem: - "Fatty acid biosynthesis" From d2132da8eae7e97646f024444f58819141bcefee Mon Sep 17 00:00:00 2001 From: Jonathan Robinson Date: Wed, 16 Nov 2022 08:57:18 +0100 Subject: [PATCH 3/3] fix: remove newly orphaned mets no longer involved in any rxns --- .../deprecatedMetabolites.tsv | 4 +++ model/Human-GEM.yml | 32 ------------------- model/metabolites.tsv | 4 --- 3 files changed, 4 insertions(+), 36 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 6219bba9..44e20a15 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2184,3 +2184,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM10033s" "MAM10033" "" "" "" "" "5283821" "" "" "" "" "" "" "m10033s" "MAM10034s" "MAM10034" "" "" "" "" "121933" "" "" "" "" "" "" "m10034s" "MAM10041s" "MAM10041" "" "" "" "" "119046" "" "" "" "" "" "" "m10041s" +"MAM01596l" "MAM01596" "co2" "C00011" "HMDB01967" "CHEBI:16526" "280" "" "" "HC00021" "co2" "MNXM13" "" "m01596l" +"MAM02444l" "MAM02444" "malcoa" "C00083" "HMDB01175" "CHEBI:15531" "10663" "LMFA07050031" "" "HC00086" "malcoa" "MNXM40" "" "m02444l" +"MAM02678l" "MAM02678" "pmtcoa" "C00154" "HMDB01338" "CHEBI:15525" "15667" "LMFA07050002" "" "HC00150" "pmtcoa" "MNXM88" "" "m02678l" +"MAM00890l" "MAM00890" "3ohodcoa" "C16216" "HMDB06498" "CHEBI:50571" "22833663" "" "" "" "3ohodcoa" "MNXM513" "" "m00890l" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index d2f08afc..846c7bc7 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -46508,38 +46508,6 @@ - charge: -1 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM01596l" - - name: "CO2" - - compartment: "l" - - formula: "CO2" - - charge: 0 - - inchis: "InChI=1S/CO2/c2-1-3" - - metFrom: "Recon3D" - - !!omap - - id: "MAM00890l" - - name: "3-oxooctadecanoyl-CoA" - - compartment: "l" - - formula: "C39H64N7O18P3S" - - charge: -4 - - inchis: "" - - metFrom: "Recon3D" - - !!omap - - id: "MAM02678l" - - name: "palmitoyl-CoA" - - compartment: "l" - - formula: "C37H62N7O17P3S" - - charge: -4 - - inchis: "" - - metFrom: "Recon3D" - - !!omap - - id: "MAM02444l" - - name: "malonyl-CoA" - - compartment: "l" - - formula: "C24H33N7O19P3S" - - charge: -5 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM00890r" - name: "3-oxooctadecanoyl-CoA" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 79f5a66a..733350c6 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -5811,10 +5811,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01373x" "MAM01373" "" "C08281" "HMDB00944" "CHEBI:28941" "8215" "LMFA01010022" "" "" "docosac" "MNXM162817;MNXM7102" "" "m01373p" "MAM02385m" "MAM02385" "lgnc" "C08320" "HMDB02003" "CHEBI:28866" "11197" "LMFA01010024" "" "HC01788" "lgnc" "MNXM3297;MNXM8841" "" "m02385m" "MAM02385x" "MAM02385" "lgnc" "C08320" "HMDB02003" "CHEBI:28866" "11197" "LMFA01010024" "" "HC01788" "lgnc" "MNXM3297;MNXM8841" "" "m02385p" -"MAM01596l" "MAM01596" "co2" "C00011" "HMDB01967" "CHEBI:16526" "280" "" "" "HC00021" "co2" "MNXM13" "" "m01596l" -"MAM00890l" "MAM00890" "3ohodcoa" "C16216" "HMDB06498" "CHEBI:50571" "22833663" "" "" "" "3ohodcoa" "MNXM513" "" "m00890l" -"MAM02678l" "MAM02678" "pmtcoa" "C00154" "HMDB01338" "CHEBI:15525" "15667" "LMFA07050002" "" "HC00150" "pmtcoa" "MNXM88" "" "m02678l" -"MAM02444l" "MAM02444" "malcoa" "C00083" "HMDB01175" "CHEBI:15531" "10663" "LMFA07050031" "" "HC00086" "malcoa" "MNXM40" "" "m02444l" "MAM00890r" "MAM00890" "3ohodcoa" "C16216" "HMDB06498" "CHEBI:50571" "22833663" "" "" "" "3ohodcoa" "MNXM513" "" "m00890r" "MAM00793r" "MAM00793" "" "" "" "" "24906329" "" "CE2248" "" "CE2248" "MNXM1309" "" "m00793r" "MAM00057n" "MAM00057" "od2coa" "C16218" "HMDB06529" "CHEBI:50570" "53477850" "LMFA07050055" "" "" "od2coa" "MNXM954" "" "m00057n"