From 578bd9d3a89aa53efb579bd1bf653614fadca04e Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 5 Jun 2023 12:20:30 -0400 Subject: [PATCH 1/5] fix: add GPR and reference for MAR08666 --- model/Human-GEM.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 1b8125db..f6a0750f 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -94505,11 +94505,11 @@ - MAM02819m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "" + - gene_reaction_rule: "ENSG00000125246" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.1.3.25" - - references: "" + - references: "PMID:24334609" - subsystem: - "C5-branched dibasic acid metabolism" - confidence_score: 0 From a822e71f6cc81e4bd5c5a2cfd48b4a822865ce29 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 5 Jun 2023 12:27:06 -0400 Subject: [PATCH 2/5] fix: add new reaction MAR20111 to represent malate synthase activity of CLYBL --- model/Human-GEM.yml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index f6a0750f..d8168227 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -307401,6 +307401,25 @@ - subsystem: - "Miscellaneous" - confidence_score: 0 + - !!omap + - id: "MAR20111" + - name: "MAR20111" + - metabolties: !!omap + - MAM1261m: -1 + - MAM01597m: 1 + - MAM02007m: -1 + - MAM02040m: -1 + - MAM02439m: 1 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000125246" + - rxnNotes: "" + - rxnFrom: "" + - eccodes: "2.3.3.9" + - references: "PMID:24334609" + - subsystem: + - "Miscellaneous" + - confidence_score: 0 - genes: - !!omap - id: "ENSG00000000419" From a786838020d9dcb71bbf86ccc6fe54078b36c889 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 5 Jun 2023 12:28:32 -0400 Subject: [PATCH 3/5] fix: remove inaccurate reactions MAR05294 and MAR11421 --- model/Human-GEM.yml | 34 ---------------------------------- 1 file changed, 34 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index d8168227..71e98b65 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -94905,23 +94905,6 @@ - subsystem: - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism" - confidence_score: 0 - - !!omap - - id: "MAR05294" - - name: "citrate oxaloacetate-lyase (forming acetate from the pro-S carboxymethyl group of citrate)" - - metabolites: !!omap - - MAM01252m: 1 - - MAM01587m: -1 - - MAM02633m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125246" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "4.1.-.-" - - references: "PMID:11741334" - - subsystem: - - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism" - - confidence_score: 0 - !!omap - id: "MAR06413" - name: "" @@ -274056,23 +274039,6 @@ - subsystem: - "Exchange/demand reactions" - confidence_score: 0 - - !!omap - - id: "MAR11421" - - name: "Citrate Lyase" - - metabolites: !!omap - - MAM01252c: 1 - - MAM01587c: -1 - - MAM02633c: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125246" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "4.1.3.6" - - references: "PMID:11741334" - - subsystem: - - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism" - - confidence_score: 0 - !!omap - id: "MAR11422" - name: "Exchange of Galactitol" From 719c9be1f44c649c3ad0f3bd8b675e68d4402172 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 5 Jun 2023 12:32:14 -0400 Subject: [PATCH 4/5] fix: update reaction data files accordingly --- data/deprecatedIdentifiers/deprecatedReactions.tsv | 2 ++ model/reactions.tsv | 3 +-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 053ee989..f785addf 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -103,3 +103,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04411" "" "PIt8" "" "" "" "PIt8" "MNXR102875" "HMR_4911" "RCR40976" "" 0 "" "" "PIt8" "MAR08749" "" "H2CO3D2" "" "" "" "HMR_8749" "MNXR100483" "HMR_8749" "RCR14128" "" 1 "" "" "HMR_8749" "MAR08750" "" "H2CO3D2m" "" "" "" "HMR_8750" "MNXR100483" "HMR_8750" "RCR14129" "" 1 "" "" "HMR_8750" +"MAR05294" "R00362" "" "R00362C" "r1109" "" "r1109" "MNXR96731" "HMR_5294" "RCR11670" "" 0 "RHEA:10761" "RHEA:10760" "HMR_5294" +"MAR11421" "" "CITL" "" "" "" "CITL" "MNXR96731" "" "" "" 0 "RHEA:10761" "RHEA:10760" "CITL" diff --git a/model/reactions.tsv b/model/reactions.tsv index 7000c233..7aef1f59 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1344,7 +1344,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04465" "R01392" "HPYRRy" "R01392C" "r0327" "" "HPYRRy" "MNXR100336" "HMR_4465" "RCR11666" "" 0 "" "RHEA:18657" "HMR_4465" "MAR04589" "R01900" "" "R01900C" "r0426" "" "r0426" "MNXR105342;MNXR95387" "HMR_4589" "RCR10352" "" 0 "" "RHEA:22144" "HMR_4589" "MAR04652" "R02164" "r0509" "R02164C" "r0509" "" "r0509" "MNXR107340" "HMR_4652" "RCR14481" "" 0 "" "RHEA:13713" "HMR_4652" -"MAR05294" "R00362" "" "R00362C" "r1109" "" "r1109" "MNXR96731" "HMR_5294" "RCR11670" "" 0 "RHEA:10761" "RHEA:10760" "HMR_5294" "MAR06413" "R03316" "" "R03316M" "r0620" "" "r0620" "MNXR105357;MNXR108089" "HMR_6413" "RCR11672" "" 0 "" "" "HMR_6413" "MAR06414" "R02570" "" "R02570C" "r0556" "" "r0556" "MNXR107585;MNXR95656" "HMR_6414" "RCR14482" "" 0 "" "RHEA:15213" "HMR_6414" "MAR07704" "R00466" "GLXO2p" "" "" "" "GLXO2p" "MNXR100305" "HMR_7704" "RCR10605" "" 0 "" "RHEA:14837" "HMR_7704" @@ -11208,7 +11207,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR11418" "" "URIt2" "" "" "" "URIt2r" "MNXR105166" "" "" "" 0 "RHEA:29954" "RHEA:29951" "URIt2r" "MAR11419" "" "EX_ind3ac_e" "" "" "" "EX_ind3ac[e]" "MNXR98679" "" "" "" 0 "" "" "EX_ind3ac[e]" "MAR11420" "" "EX_nh4_e" "" "" "" "EX_nh4[e]" "MNXR98786" "" "" "" 0 "" "" "EX_nh4[e]" -"MAR11421" "" "CITL" "" "" "" "CITL" "MNXR96731" "" "" "" 0 "RHEA:10761" "RHEA:10760" "CITL" "MAR11422" "" "EX_galt_e" "" "" "" "EX_galt[e]" "MNXR98554" "" "" "" 0 "" "" "EX_galt[e]" "MAR11423" "" "EX_glcr_e" "" "" "" "EX_glcr[e]" "MNXR98575" "" "" "" 0 "" "" "EX_glcr[e]" "MAR11424" "" "EX_glcur_e" "" "" "" "EX_glcur[e]" "MNXR98577" "" "" "" 0 "" "" "EX_glcur[e]" @@ -13091,3 +13089,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20108" "" "HBZOPT10m;R_HBZOPT10m" "" "" "" "" "MNXR100567" "" "" "" 0 "RHEA:44564" "" "" "MAR20109" "" "HBZOPT10m;R_HBZOPT10m" "" "" "" "" "MNXR100567" "" "" "" 0 "RHEA:44564" "" "" "MAR20110" "" "" "" "" "" "" "MNXR102097" "" "" "" 0 "RHEA:15642" "RHEA:15641" "" +"MAR20111" "R00472" "" "" "" "" "MNXR188337" "" "" "" 0 "RHEA:18182" "RHEA:18181" "" From 3e25c4eac72fc265b5d63bd0b82d7b0fc10b155c Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 5 Jun 2023 12:40:18 -0400 Subject: [PATCH 5/5] fix: added missing column to last row of model/reactions.tsv --- model/reactions.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/reactions.tsv b/model/reactions.tsv index 7aef1f59..9ff9475f 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -13089,4 +13089,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20108" "" "HBZOPT10m;R_HBZOPT10m" "" "" "" "" "MNXR100567" "" "" "" 0 "RHEA:44564" "" "" "MAR20109" "" "HBZOPT10m;R_HBZOPT10m" "" "" "" "" "MNXR100567" "" "" "" 0 "RHEA:44564" "" "" "MAR20110" "" "" "" "" "" "" "MNXR102097" "" "" "" 0 "RHEA:15642" "RHEA:15641" "" -"MAR20111" "R00472" "" "" "" "" "MNXR188337" "" "" "" 0 "RHEA:18182" "RHEA:18181" "" +"MAR20111" "R00472" "" "" "" "" "" "MNXR188337" "" "" "" 0 "RHEA:18182" "RHEA:18181" ""