From dcc26907fe633f41b321f4718806824174c0516a Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sat, 14 Oct 2023 22:04:38 +0200 Subject: [PATCH 1/6] fix: remove ENSG00000159423 from MAR00051 - The substrate of ENSG00000159423 (ALDH4A1) is known as L-glutamate 5-semialdehyde, instead of 5-hydroxyindoleacetaldehyde --- 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 c6a46e87..250ee363 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -218228,7 +218228,7 @@ - MAM02553m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124 or ENSG00000159423" + - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.5.1.12" From 1eb71c613fcf4cdad4158ef5d34e6043130943bc Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sat, 14 Oct 2023 23:01:57 +0200 Subject: [PATCH 2/6] fix: remove MAR08564 and MAR08565 - remove MAR08564+MAR08565 that are duplicate to MAR04222 - reverse reaction direction of MAR04222 --- model/Human-GEM.yml | 45 +++++---------------------------------------- 1 file changed, 5 insertions(+), 40 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 250ee363..951ca6f4 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -81699,41 +81699,6 @@ - subsystem: - "Tryptophan metabolism" - confidence_score: 0 - - !!omap - - id: "MAR08564" - - name: "" - - metabolites: !!omap - - MAM00926c: 1 - - MAM01306c: -1 - - MAM01974c: 1 - - MAM02319c: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000109576 or ENSG00000137944 or ENSG00000171097" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "2.6.1.7" - - references: "" - - subsystem: - - "Tryptophan metabolism" - - confidence_score: 0 - - !!omap - - id: "MAR08565" - - name: "" - - metabolites: !!omap - - MAM00926c: -1 - - MAM00990c: 1 - - MAM02040c: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "" - - subsystem: - - "Tryptophan metabolism" - - confidence_score: 0 - !!omap - id: "MAR08566" - name: "" @@ -82834,11 +82799,11 @@ - id: "MAR04222" - name: "" - metabolites: !!omap - - MAM00990c: -1 - - MAM01306c: 1 - - MAM01974c: -1 - - MAM02040c: -1 - - MAM02319c: 1 + - MAM00990c: 1 + - MAM01306c: -1 + - MAM01974c: 1 + - MAM02040c: 1 + - MAM02319c: -1 - lower_bound: -1000 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000109576 or ENSG00000137944 or ENSG00000171097" From f739d41a991542489f63cdf0106d277d53ff98e7 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sat, 14 Oct 2023 23:07:49 +0200 Subject: [PATCH 3/6] fix: remove ENSG00000109576 from MAR04222 - ENSG00000109576 (AADAT) is localized in mitochondrion, not cytosol --- 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 951ca6f4..48a4900d 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -82806,7 +82806,7 @@ - MAM02319c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000109576 or ENSG00000137944 or ENSG00000171097" + - gene_reaction_rule: "ENSG00000137944 or ENSG00000171097" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.6.1.7" From 34c2da957c1620563bbac721b0d129f6dec09203 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sat, 14 Oct 2023 23:18:33 +0200 Subject: [PATCH 4/6] doc: sync deletion of MAR08564+MAR08565 to data files --- data/deprecatedIdentifiers/deprecatedReactions.tsv | 4 +++- model/reactions.tsv | 4 +--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 5524225a..f4b34adf 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -238,4 +238,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR07771" "" "NADtpu" "" "" "" "NADtx" "MNXR101881" "HMR_7771" "RCR20023" "" 0 "" "" "HMR_7771" "MAR07782" "" "ADPtx" "" "" "" "ADPtx" "MNXR95484" "HMR_7782" "RCR20201" "" 0 "" "" "HMR_7782" "MAR07783" "" "AMPtp" "" "" "" "AMPtp" "MNXR95830" "HMR_7783" "RCR20046" "" 0 "" "" "HMR_7783" -"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790" \ No newline at end of file +"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790" +"MAR08564" "" "KYNAKGAT" "" "" "" "KYNAKGAT" "MNXR100948" "HMR_8564" "RCR11356" "" 0 "" "" "HMR_8564" +"MAR08565" "R03445" "KYNATESYN" "" "" "" "KYNATESYN" "MNXR100949" "HMR_8565" "RCR11357" "" 0 "" "RHEA:42452" "HMR_8565" diff --git a/model/reactions.tsv b/model/reactions.tsv index 34c5374f..47894bb3 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -748,8 +748,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR08091" "" "3HXKYNDCL" "" "" "" "3HXKYNDCL" "MNXR94906" "HMR_8091" "RCR11354" "" 0 "" "" "HMR_8091" "MAR08092" "R04907" "3HXKYNOXDA" "" "" "" "3HXKYNOXDA" "MNXR94907" "HMR_8092" "RCR11355" "" 0 "" "" "HMR_8092" "MAR08563" "R02678" "ALDD20xm" "" "" "" "ALDD20xm" "MNXR95744" "HMR_8563" "RCR10320" "" 0 "" "RHEA:30867" "HMR_8563" -"MAR08564" "" "KYNAKGAT" "" "" "" "KYNAKGAT" "MNXR100948" "HMR_8564" "RCR11356" "" 0 "" "" "HMR_8564" -"MAR08565" "R03445" "KYNATESYN" "" "" "" "KYNATESYN" "MNXR100949" "HMR_8565" "RCR11357" "" 0 "" "RHEA:42452" "HMR_8565" "MAR08566" "" "MELATNOX" "" "" "" "MELATNOX" "MNXR101458" "HMR_8566" "RCR11358" "" 0 "" "" "HMR_8566" "MAR03935" "R06982" "r1377" "" "r1377" "" "r1377" "MNXR105462;MNXR99239" "HMR_3935" "RCR11359" "" 0 "" "RHEA:22488" "HMR_3935" "MAR04681" "R00699" "" "" "" "" "PHYCBOXL" "MNXR102650" "HMR_4681" "RCR10321" "" 0 "" "RHEA:19717" "HMR_4681" @@ -808,7 +806,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04218" "R03936" "LFORKYNHYD" "R03936C" "r0646" "" "LFORKYNHYD" "MNXR101060;MNXR108539" "HMR_4218" "RCR11391" "" 0 "" "" "HMR_4218" "MAR04219" "R00988" "" "R00988C" "r0239" "" "r0239" "MNXR105316;MNXR106774" "HMR_4219" "RCR11392" "" 0 "" "" "HMR_4219" "MAR04220" "R01960" "KYN3OX" "R01960C" "r0455" "" "KYN3OX" "MNXR100947" "HMR_4220" "RCR11393" "" 0 "RHEA:20548" "RHEA:20545" "HMR_4220" -"MAR04222" "" "" "RE1233C" "" "" "RE1233C" "" "HMR_4222" "RCR11394" "" 0 "" "" "HMR_4222" +"MAR04222" "" "" "RE1233C" "" "" "RE1233C" "" "HMR_4222" "RCR11394" "" 0 "" "" "HMR_4222;MAR08564+MAR08565" "MAR04224" "R00987" "KYN" "R00987C" "r0238" "" "KYN" "MNXR100946" "HMR_4224" "RCR11395" "" 0 "" "RHEA:16813" "HMR_4224" "MAR04225" "R02668" "HKYNH" "R02668C" "r0563" "" "HKYNH" "MNXR100656" "HMR_4225" "RCR10534" "" 0 "" "RHEA:25143" "HMR_4225" "MAR04227" "R02670" "" "" "" "" "HMR_4227" "MNXR107655" "HMR_4227" "RCR14355" "" 0 "" "" "HMR_4227" From e503177ae29c3ff25c473a846177bc9343ce2700 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sat, 14 Oct 2023 23:26:19 +0200 Subject: [PATCH 5/6] fix/doc: make MAR04222 and MAR02765 irreversible based on Uniprot - make MAR04222 and MAR02765 irreversible based on Uniprot annotation - update their Rhea ids --- model/Human-GEM.yml | 4 ++-- model/reactions.tsv | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 48a4900d..e02481cf 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -82804,7 +82804,7 @@ - MAM01974c: 1 - MAM02040c: 1 - MAM02319c: -1 - - lower_bound: -1000 + - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000137944 or ENSG00000171097" - rxnNotes: "" @@ -230309,7 +230309,7 @@ - MAM01974m: 1 - MAM02040m: 1 - MAM02319m: -1 - - lower_bound: -1000 + - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000109576 or ENSG00000137944" - rxnNotes: "" diff --git a/model/reactions.tsv b/model/reactions.tsv index 47894bb3..7ec1a1fb 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -806,7 +806,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04218" "R03936" "LFORKYNHYD" "R03936C" "r0646" "" "LFORKYNHYD" "MNXR101060;MNXR108539" "HMR_4218" "RCR11391" "" 0 "" "" "HMR_4218" "MAR04219" "R00988" "" "R00988C" "r0239" "" "r0239" "MNXR105316;MNXR106774" "HMR_4219" "RCR11392" "" 0 "" "" "HMR_4219" "MAR04220" "R01960" "KYN3OX" "R01960C" "r0455" "" "KYN3OX" "MNXR100947" "HMR_4220" "RCR11393" "" 0 "RHEA:20548" "RHEA:20545" "HMR_4220" -"MAR04222" "" "" "RE1233C" "" "" "RE1233C" "" "HMR_4222" "RCR11394" "" 0 "" "" "HMR_4222;MAR08564+MAR08565" +"MAR04222" "" "" "RE1233C" "" "" "RE1233C" "" "HMR_4222" "RCR11394" "" 0 "RHEA:65561" "RHEA:65560" "HMR_4222;MAR08564+MAR08565" "MAR04224" "R00987" "KYN" "R00987C" "r0238" "" "KYN" "MNXR100946" "HMR_4224" "RCR11395" "" 0 "" "RHEA:16813" "HMR_4224" "MAR04225" "R02668" "HKYNH" "R02668C" "r0563" "" "HKYNH" "MNXR100656" "HMR_4225" "RCR10534" "" 0 "" "RHEA:25143" "HMR_4225" "MAR04227" "R02670" "" "" "" "" "HMR_4227" "MNXR107655" "HMR_4227" "RCR14355" "" 0 "" "" "HMR_4227" @@ -8724,7 +8724,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR02751" "" "RE1134M" "" "" "" "RE1134M" "MNXR102255" "" "" "" 0 "" "" "RE1134M" "MAR02756" "" "" "" "" "" "RE1135G" "" "" "" "" 0 "" "" "RE1135G" "MAR02763" "" "" "" "" "" "RE1135L" "" "" "" "" 0 "" "" "RE1135L" -"MAR02765" "" "" "" "" "" "RE1233M" "" "" "" "" 0 "" "" "RE1233M" +"MAR02765" "" "" "" "" "" "RE1233M" "" "" "" "" 0 "RHEA:65561" "RHEA:65560" "RE1233M" "MAR02767" "" "RE1309M" "" "" "" "RE1309M" "MNXR103507" "" "" "" 0 "" "" "RE1309M" "MAR02779" "" "RE1342C" "" "" "" "RE1342C" "MNXR103511" "" "" "" 0 "" "" "RE1342C" "MAR02781" "" "RE1447M" "" "" "" "RE1447M" "MNXR102717" "" "" "" 0 "" "" "RE1447M" From ca672c9923eb145e0ef47073f5df2e8846f05bfe Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sat, 14 Oct 2023 23:32:43 +0200 Subject: [PATCH 6/6] doc: sync deletion of MAM00926c - MAM00926c becomes deprecated after removal of MAR08564+MAR08565 --- data/deprecatedIdentifiers/deprecatedMetabolites.tsv | 1 + model/Human-GEM.yml | 8 -------- model/metabolites.tsv | 1 - 3 files changed, 1 insertion(+), 9 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 193acd1e..56337256 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2247,3 +2247,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02757l" "MAM02757" "" "" "" "" "" "" "" "" "M02757" "" "m02757l" "m02757l" "MAM02757n" "MAM02757" "" "" "" "" "" "" "" "" "M02757" "" "m02757n" "m02757n" "MAM01816n" "MAM01816" "" "" "" "" "" "PROTEIN" "" "" "M01816" "" "m01816n" "m01816n" +"MAM00926c" "MAM00926" "4aphdob" "C01252" "HMDB0000978" "CHEBI:17442" "472" "" "" "" "4aphdob" "MNXM163204" "m00926c" "m00926c" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index e02481cf..1472f093 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -11729,14 +11729,6 @@ - charge: -1 - inchis: "" - metFrom: "HMRdatabase" - - !!omap - - id: "MAM00926c" - - name: "4-(2-aminophenyl)-2,4-dioxobutanoate" - - compartment: "c" - - formula: "C10H8NO4" - - charge: -1 - - inchis: "" - - metFrom: "HMRdatabase" - !!omap - id: "MAM00927c" - name: "4-(methylnitrosamino)-1-(1-oxido-3-pyridinyl)-1-butanone" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 63fa75cc..076825d0 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -1464,7 +1464,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00923c" "MAM00923" "cala" "C02642" "HMDB0000026" "CHEBI:18261" "111" "" "" "HC00975" "cala" "MNXM802" "m00923c" "m00923c" "MAM00924c" "MAM00924" "42A3HP24DB" "C05645" "" "" "440741" "" "" "HC01547" "42A3HP24DB" "MNXM163203;MNXM4997" "m00924c" "m00924c" "MAM00925c" "MAM00925" "" "" "" "" "10948689" "" "CE3086" "" "CE3086" "MNXM166294" "m00925c" "m00925c" -"MAM00926c" "MAM00926" "4aphdob" "C01252" "HMDB0000978" "CHEBI:17442" "472" "" "" "" "4aphdob" "MNXM163204" "m00926c" "m00926c" "MAM00927c" "MAM00927" "" "C19602" "" "" "" "" "" "" "M00927" "MNXM14691" "m00927c" "m00927c" "MAM00928c" "MAM00928" "" "C19605" "" "" "" "" "" "" "M00928" "MNXM14692" "m00928c" "m00928c" "MAM00929c" "MAM00929" "" "C19574" "" "" "" "" "" "" "M00929" "MNXM4356" "m00929c" "m00929c"