From f554fa2021a21fefc2227f02974613af72215a98 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 6 Dec 2023 16:37:49 -0500 Subject: [PATCH 1/3] fix: remove MAR03748 and MAR03780 and merge annotations in reactions.tsv into MAR06416/7 and MAR06419/20 --- .../deprecatedReactions.tsv | 3 ++ model/Human-GEM.yml | 40 ------------------- model/reactions.tsv | 10 ++--- 3 files changed, 7 insertions(+), 46 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index c726bad6..44dbcdd5 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -262,3 +262,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04239" "R01933" "2OXOADOXm" "R01933M" "r0448" "" "2OXOADOXm" "MNXR94818" "HMR_4239" "RCR11332" "" 0 "RHEA:30796" "RHEA:30795" "HMR_4239" "MAR04940" "" "" "" "r0885" "" "r0885" "MNXR105402" "HMR_4940" "RCR20265" "2.A.29.2.7" 0 "" "" "HMR_4940" "MAR06391" "" "" "" "r2520" "" "r2520" "MNXR106328" "HMR_6391" "RCR20063" "" 0 "" "" "HMR_6391" +"MAR03748" "R01210" "OIVD2m" "R03171M" "r0600" "" "OIVD2m" "MNXR102173;MNXR107999" "HMR_3748" "RCR14420" "" 0 "" "RHEA:13997" "HMR_3748" +"MAR03780" "R03171" "OIVD3m" "R03171M" "r0602" "" "OIVD3m" "MNXR102174;MNXR107999" "HMR_3780" "RCR10345" "" 0 "" "RHEA:30907" "HMR_3780" + diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8ee075f6..11c7d9aa 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -87297,26 +87297,6 @@ - subsystem: - "Metabolism of other amino acids" - confidence_score: 0 - - !!omap - - id: "MAR03748" - - name: "3-methyl-2-oxobutanoate:NAD+ oxidoreductase (CoA-mehtylpropanoylating)" - - metabolites: !!omap - - MAM00824m: -1 - - MAM01596m: 1 - - MAM01597m: -1 - - MAM02180m: 1 - - MAM02552m: -1 - - MAM02553m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000083123 and ENSG00000142046 and ENSG00000248098" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "1.2.1.25" - - references: "" - - subsystem: - - "Valine, leucine, and isoleucine metabolism" - - confidence_score: 0 - !!omap - id: "MAR03753" - name: "(S)-3-Hydroxyisobutyryl-CoA hydro-lyase" @@ -87430,26 +87410,6 @@ - subsystem: - "Valine, leucine, and isoleucine metabolism" - confidence_score: 0 - - !!omap - - id: "MAR03780" - - name: "(S)-3-methyl-2-oxopentanoate:NAD+ 2-oxidoreductase (CoA-methylbutanoylating)" - - metabolites: !!omap - - MAM00663m: 1 - - MAM00669m: -1 - - MAM01596m: 1 - - MAM01597m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000083123 and ENSG00000142046 and ENSG00000248098" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "1.2.1.25" - - references: "" - - subsystem: - - "Valine, leucine, and isoleucine metabolism" - - confidence_score: 0 - !!omap - id: "MAR03785" - name: "(2S,3S)-3-Hydroxy-2-methylbutanoyl-CoA hydro-liase" diff --git a/model/reactions.tsv b/model/reactions.tsv index 7c808f4e..81b2c7af 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -786,9 +786,9 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03778" "R01090" "ILETAm" "R01090C" "r0264" "" "ILETAm" "MNXR96228;MNXR96229" "HMR_3778" "RCR11380" "" 0 "" "RHEA:18321" "HMR_3778" "MAR03795" "R00922" "MMSAD1m" "R00922M" "r0223" "" "MMSAD1m" "MNXR101662" "HMR_3795" "RCR10324" "" 0 "" "RHEA:20804" "HMR_3795" "MAR04797" "R03869" "" "R03869C" "r0642" "" "r0642" "MNXR105358;MNXR95762" "HMR_4797" "RCR10533" "" 0 "" "RHEA:31043" "HMR_4797" -"MAR06417" "R02662" "" "RE3326M" "r0561" "" "RE3326M;r0561" "MNXR107649;MNXR97451" "HMR_6417" "RCR14349" "" 0 "" "RHEA:18865" "HMR_6417" -"MAR06419" "R04225" "" "R04225C" "r0670" "" "r0670" "MNXR108745;MNXR94911" "HMR_6419" "RCR11381" "" 0 "" "" "HMR_6419" -"MAR06420" "R03174" "" "" "r0604" "" "r0604" "MNXR108002;MNXR97450" "HMR_6420" "RCR14350" "" 0 "" "" "HMR_6420" +"MAR06417" "R02662" "OIVD2m" "RE3326M;R03171M" "r0561;r0600" "" "RE3326M;r0561;OIVD2m" "MNXR107649;MNXR97451" "HMR_6417;HMR_3748" "RCR14349;RCR14420" "" 0 "" "RHEA:18865" "HMR_6417;HMR_3748;MAR03748" +"MAR06419" "R04225" "OIVD3m" "R04225C;R03171M" "r0670;r0602" "" "r0670;OIVD3m" "MNXR108745;MNXR94911" "HMR_6419;HMR_3780" "RCR11381;RCR10345" "" 0 "" "" "HMR_6419;HMR_3780;MAR03780" +"MAR06420" "R03174" "OIVD3m" "R03171M" "r0604;r0602" "" "r0604;OIVD3m" "MNXR108002;MNXR97450" "HMR_6420;HMR_3780" "RCR14350;RCR10345" "" 0 "" "" "HMR_6420;HMR_3780;MAR03780" "MAR06421" "R01702;R01651" "OIVD1m" "R01702C;R03171M" "r0386;r0601" "" "r0386;OIVD1m" "MNXR107132;MNXR95029;MNXR102172;MNXR107999" "HMR_6421;HMR_3767" "RCR11382;RCR14422" "" 0 "" "RHEA:25177" "HMR_6421;HMR_3767;MAR03767_1" "MAR06422" "R04097;R01651" "OIVD1m" "R0317M" "r0656;r0601" "" "r0656;OIVD1m" "MNXR108654;MNXR97452;MNXR102172;MNXR107999" "HMR_6422;HMR_3767" "RCR14351;RCR14422" "" 0 "" "RHEA:25177" "HMR_6422;MAR03767_2" "MAR06923" "R01090" "LEUTA" "" "" "" "LEUTA" "MNXR96229" "HMR_6923" "RCR10325" "" 0 "" "RHEA:18321" "HMR_6923" @@ -1047,20 +1047,18 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR08640" "R04939" "DNDPt11m" "" "" "" "DNAMTSEn" "MNXR97629" "HMR_8640" "RCR14417" "" 0 "" "" "HMR_8640" "MAR08689" "R02923" "DASCBH" "" "" "" "DARGOp" "MNXR97151" "HMR_8689" "RCR14418" "" 0 "" "" "HMR_8689" "MAR08690" "R02457" "DPCOAPP" "" "" "" "DORNOp" "MNXR97763" "HMR_8690" "RCR14419" "" 0 "" "" "HMR_8690" -"MAR03748" "R01210" "OIVD2m" "R03171M" "r0600" "" "OIVD2m" "MNXR102173;MNXR107999" "HMR_3748" "RCR14420" "" 0 "" "RHEA:13997" "HMR_3748" "MAR03753" "R04224" "ECOAH2m" "R04224M" "r0669" "" "ECOAH12m;r0669" "MNXR97885" "HMR_3753" "RCR11518" "" 0 "" "RHEA:31175" "HMR_3753" "MAR03755" "R03352" "3HBCOAHLm;r0779" "R03352M" "r0779" "" "3HBCOAHLm;r0779" "MNXR108112;MNXR94891" "HMR_3755" "RCR11519" "" 0 "" "RHEA:20888" "3HBCOAHLm;HMR_3755;MAR00042" "MAR03759" "R03869" "r0643" "R03869C" "r0643" "" "r0643" "MNXR105358;MNXR95762" "HMR_3759" "RCR10556" "" 0 "" "RHEA:31043" "HMR_3759" "MAR03763" "R02764" "r0571" "" "r0571" "" "" "MNXR105351" "HMR_3763" "RCR10557" "" 0 "" "RHEA:17345" "HMR_3763" "MAR03773" "R04138" "MCCCrm" "R04138M" "r0658" "" "MCCCrm" "MNXR101411" "HMR_3773" "RCR11520" "" 0 "" "RHEA:13589" "HMR_3773" "MAR03775" "R02085" "MGCHrm" "R02085M" "r0490" "" "MGCHrm" "MNXR101513;MNXR107307" "HMR_3775" "RCR11521" "" 0 "" "RHEA:21536" "HMR_3775" -"MAR03780" "R03171" "OIVD3m" "R03171M" "r0602" "" "OIVD3m" "MNXR102174;MNXR107999" "HMR_3780" "RCR10345" "" 0 "" "RHEA:30907" "HMR_3780" "MAR03785" "R04204" "ECOAH9m" "R04204M" "r0665" "" "ECOAH9m" "MNXR97894" "HMR_3785" "RCR11522" "" 0 "" "RHEA:31119" "HMR_3785" "MAR03790" "R03871" "r0644" "R03871C" "r0644" "" "r0644" "MNXR105359;MNXR108490" "HMR_3790" "RCR10558" "" 0 "" "" "HMR_3790" "MAR03792" "R02048" "" "R02048M" "r0483" "" "3AIBTm;r0483" "MNXR105346" "HMR_3792" "RCR11523" "" 0 "" "" "HMR_3792" "MAR03796" "R00926" "" "R00926C" "r0221" "" "r0221" "MNXR105315;MNXR106754" "HMR_3796" "RCR10119" "" 0 "" "" "HMR_3796" "MAR03823" "R04203" "HACD9m" "R04203M" "r0664" "" "HACD9m" "MNXR100550" "HMR_3823" "RCR11524" "" 0 "" "RHEA:13281" "HMR_3823" -"MAR06416" "R01701" "" "R01701C" "r0385" "" "r0385" "MNXR107131;MNXR94910" "HMR_6416" "RCR11525" "" 0 "" "RHEA:13457" "HMR_6416" +"MAR06416" "R01701" "OIVD2m" "R01701C;R03171M" "r0385;r0600" "" "r0385;OIVD2m" "MNXR107131;MNXR94910" "HMR_6416;HMR_3748" "RCR11525;RCR14420" "" 0 "" "RHEA:13457" "HMR_6416;HMR_3748;MAR03748" "MAR03986" "" "" "" "r1374" "" "r1374" "MNXR105461" "HMR_3986" "RCR30265" "" 0 "" "" "HMR_3986" "MAR03988" "R00022" "" "R00022C" "r0013" "" "r0013" "MNXR100746;MNXR95628" "HMR_3988" "RCR11526" "" 0 "" "RHEA:30671" "HMR_3988" "MAR04124" "R01384" "UDPGLDCg" "R01384C" "r0326" "" "HMR_4124" "MNXR105068" "HMR_4124" "RCR11527" "" 0 "" "RHEA:23916" "HMR_4124" From de0eac488c1b0c9ec440f54d780ea5a45dd0b5f0 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Fri, 8 Dec 2023 10:04:20 -0500 Subject: [PATCH 2/3] fix: removed MAR03422 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 23 ------- model/reactions.tsv | 65 +++++++++---------- 3 files changed, 33 insertions(+), 56 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index c726bad6..93d052de 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -262,3 +262,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04239" "R01933" "2OXOADOXm" "R01933M" "r0448" "" "2OXOADOXm" "MNXR94818" "HMR_4239" "RCR11332" "" 0 "RHEA:30796" "RHEA:30795" "HMR_4239" "MAR04940" "" "" "" "r0885" "" "r0885" "MNXR105402" "HMR_4940" "RCR20265" "2.A.29.2.7" 0 "" "" "HMR_4940" "MAR06391" "" "" "" "r2520" "" "r2520" "MNXR106328" "HMR_6391" "RCR20063" "" 0 "" "" "HMR_6391" +"MAR03422" "" "" "" "" "" "HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "HMR_3422" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 460f88a5..d1a76971 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -119154,29 +119154,6 @@ - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 - - !!omap - - id: "MAR03422" - - name: "" - - metabolites: !!omap - - MAM00093m: -1 - - MAM01261m: 11 - - MAM01597m: -10 - - MAM01802m: -5 - - MAM01803m: 5 - - MAM02039m: 10 - - MAM02040m: -10 - - MAM02552m: -10 - - MAM02553m: 10 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000060971 or ENSG00000072506 or ENSG00000072778 or ENSG00000084754 or ENSG00000115361 or ENSG00000117054 or ENSG00000127884 or ENSG00000138029 or ENSG00000138796 or ENSG00000167315 or ENSG00000177646" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "4.2.1.17;1.1.1.35;1.1.1.211;1.3.8.7;1.3.8.8;1.3.8.9;2.3.1.16" - - references: "" - - subsystem: - - "Beta oxidation of even-chain fatty acids (mitochondrial)" - - confidence_score: 0 - !!omap - id: "MAR03423" - name: "" diff --git a/model/reactions.tsv b/model/reactions.tsv index 7c808f4e..86211065 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -178,7 +178,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00719" "R08198" "" "" "" "" "HMR_0719" "MNXR111769" "HMR_0719" "RCR11097" "" 0 "" "RHEA:13449" "HMR_0719" "MAR01434" "R00238" "ACACT1r" "R00238M" "r0069" "" "ACACT1r" "MNXR95194" "HMR_1434" "RCR10465" "" 0 "RHEA:21039" "RHEA:21036" "HMR_1434" "MAR01436" "R01357" "AACOAT" "R01357M" "r0320" "" "AACOAT" "MNXR95136" "HMR_1436" "RCR10466" "" 0 "RHEA:16118" "RHEA:16117" "HMR_1436" -"MAR03163" "R01175" "ACOAD1fm" "" "" "R-HSA-77319" "ACOAD1fm" "MNXR95302" "HMR_3163" "RCR11098" "" 0 "" "RHEA:24004" "HMR_3163" +"MAR03163" "R01175" "ACOAD1fm" "" "" "R-HSA-77319" "ACOAD1fm;HMR_3422" "MNXR95302" "HMR_3163;HMR_3422" "RCR11098;RCR12667" "" 0 "" "RHEA:24004" "HMR_3163;HMR_3422;MAR03422" "MAR04461" "R01361" "BDHm" "R01361C" "r0323" "" "BDHm" "MNXR96232" "HMR_4461" "RCR10467" "" 0 "RHEA:20524" "RHEA:20521" "HMR_4461" "MAR04604" "R01978" "" "R01978C" "r0463" "" "r0463" "MNXR100660;MNXR107257" "HMR_4604" "RCR11099" "" 0 "" "RHEA:10188" "HMR_4604" "MAR05351" "R01000" "" "" "" "" "2HBO" "MNXR94796" "HMR_5351" "RCR10152" "" 0 "" "RHEA:36371" "HMR_5351" @@ -740,9 +740,9 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR08026" "" "LYSMTF2n" "" "" "" "LYSMTF2n" "MNXR101260" "HMR_8026" "RCR11349" "" 0 "" "" "HMR_8026" "MAR08027" "R04867" "LYSMTF3n" "" "" "" "LYSMTF3n" "MNXR101261" "HMR_8027" "RCR11350" "" 0 "" "RHEA:54200" "HMR_8027" "MAR08029" "" "PLYSPSer" "" "" "" "PLYSPSer" "MNXR103039" "HMR_8029" "RCR14338" "" 0 "" "" "HMR_8029" -"MAR03164" "R03026" "ECOAH1m" "R03026M" "r0588" "" "ECOAH1m" "MNXR97883" "HMR_3164" "RCR11351" "" 0 "" "RHEA:26558" "HMR_3164" -"MAR03166" "R01975" "HACD1m" "R01975M" "r0460" "" "HACD1m" "MNXR100541" "HMR_3166" "RCR11352" "" 0 "" "RHEA:30799" "HMR_3166" -"MAR03885" "R00238" "ACACT1m" "R00238M" "r0070" "" "ACACT1rm" "MNXR95194" "HMR_3885" "RCR10247" "" 0 "RHEA:21039" "RHEA:21036" "HMR_3885" +"MAR03164" "R03026" "ECOAH1m" "R03026M" "r0588" "" "ECOAH1m;HMR_3422" "MNXR97883" "HMR_3164;HMR_3422" "RCR11351;RCR12667" "" 0 "" "RHEA:26558" "HMR_3164;HMR_3422;MAR03422" +"MAR03166" "R01975" "HACD1m" "R01975M" "r0460" "" "HACD1m;HMR_3422" "MNXR100541" "HMR_3166;HMR_3422" "RCR11352;RCR12667" "" 0 "" "RHEA:30799" "HMR_3166;HMR_3422;MAR03422" +"MAR03885" "R00238" "ACACT1m" "R00238M" "r0070" "" "ACACT1rm;HMR_3422" "MNXR95194" "HMR_3885;HMR_3422" "RCR10247;RCR12667" "" 0 "RHEA:21039" "RHEA:21036" "HMR_3885;HMR_3422;MAR03422" "MAR04250" "R04293" "QUILSYN" "" "r0675" "" "QUILSYN" "MNXR103396" "HMR_4250" "RCR11353" "" 1 "" "RHEA:25147" "HMR_4250" "MAR08091" "" "3HXKYNDCL" "" "" "" "3HXKYNDCL" "MNXR94906" "HMR_8091" "RCR11354" "" 0 "" "" "HMR_8091" "MAR08092" "R04907" "3HXKYNOXDA" "" "" "" "3HXKYNOXDA" "MNXR94907" "HMR_8092" "RCR11355" "" 0 "" "" "HMR_8092" @@ -2646,17 +2646,17 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03137" "R04741" "" "R04741X" "r0722" "" "r0722" "MNXR100546" "HMR_3137" "RCR12643" "" 0 "" "RHEA:31179" "HMR_3137" "MAR03139" "R04742" "" "R04742X" "r0724" "" "r0724" "MNXR95199;MNXR95200" "HMR_3139" "RCR12644" "" 0 "RHEA:31185" "RHEA:31183" "HMR_3139" "MAR03142" "R04754" "r1451" "" "" "R-HSA-77345" "HMR_3142;r1451" "MNXR109095" "HMR_3142" "RCR12645" "" 0 "" "RHEA:28354" "HMR_3142;r1451;MAR02373" -"MAR03143" "R04744" "" "R04744X" "r0728" "" "r0728" "MNXR97889" "HMR_3143" "RCR12646" "" 0 "" "RHEA:31191" "HMR_3143" -"MAR03144" "R04743" "" "R04743X" "r0726" "" "r0726" "MNXR100545" "HMR_3144" "RCR12647" "" 0 "" "RHEA:31187" "HMR_3144" -"MAR03146" "R03778" "" "R03778X" "r0634" "" "r0634" "MNXR95198" "HMR_3146" "RCR12648" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146" -"MAR03149" "R03777" "r1448" "" "" "R-HSA-77338" "HMR_3149;r1448" "MNXR95304" "HMR_3149" "RCR12649" "" 0 "" "RHEA:30943" "HMR_3149;r1448;MAR02369" -"MAR03150" "R04746" "" "R04746M" "r0731" "" "r0731" "MNXR97888" "HMR_3150" "RCR12650" "" 0 "" "RHEA:31199" "HMR_3150" -"MAR03151" "R04745" "" "R04745M" "r0730" "" "r0730" "MNXR100544" "HMR_3151" "RCR12651" "" 0 "" "RHEA:31195" "HMR_3151" -"MAR03153" "R04747" "" "R04747M" "r0732" "" "r0732" "MNXR109092" "HMR_3153" "RCR12652" "" 0 "RHEA:31205" "RHEA:31203" "HMR_3153" -"MAR03156" "R04751" "r1450" "" "" "R-HSA-77327" "HMR_3156;r1450" "MNXR109093" "HMR_3156" "RCR12653" "" 0 "" "RHEA:31207" "HMR_3156;r1450;MAR02372" -"MAR03157" "R04749" "" "R04749M" "r0734" "" "r0734" "MNXR97886" "HMR_3157" "RCR12654" "" 0 "" "RHEA:30547" "HMR_3157" -"MAR03158" "R04748" "" "R04748M" "r0733" "R-HSA-77323" "r0733" "MNXR100543" "HMR_3158" "RCR12655" "" 0 "" "RHEA:31143" "HMR_3158" -"MAR03160" "R01177" "" "R01177M" "r0287" "R-HSA-77321" "r0287" "MNXR95196" "HMR_3160" "RCR12656" "" 0 "" "RHEA:31111" "HMR_3160" +"MAR03143" "R04744" "" "R04744X" "r0728" "" "r0728;HMR_3422" "MNXR97889" "HMR_3143;HMR_3422" "RCR12646;RCR12667" "" 0 "" "RHEA:31191" "HMR_3143;HMR_3422;MAR03422" +"MAR03144" "R04743" "" "R04743X" "r0726" "" "r0726;HMR_3422" "MNXR100545" "HMR_3144;HMR_3422" "RCR12647;RCR12667" "" 0 "" "RHEA:31187" "HMR_3144;HMR_3422;MAR03422" +"MAR03146" "R03778" "" "R03778X" "r0634" "" "r0634;HMR_3422" "MNXR95198" "HMR_3146;HMR_3422" "RCR12648;RCR12667" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146;HMR_3422;MAR03422" +"MAR03149" "R03777" "r1448" "" "" "R-HSA-77338" "HMR_3149;r1448;HMR_3422" "MNXR95304" "HMR_3149;HMR_3422" "RCR12649;RCR12667" "" 0 "" "RHEA:30943" "HMR_3149;r1448;MAR02369;HMR_3422;MAR03422" +"MAR03150" "R04746" "" "R04746M" "r0731" "" "r0731;HMR_3422" "MNXR97888" "HMR_3150;HMR_3422" "RCR12650;RCR12667" "" 0 "" "RHEA:31199" "HMR_3150;HMR_3422;MAR03422" +"MAR03151" "R04745" "" "R04745M" "r0730" "" "r0730;HMR_3422" "MNXR100544" "HMR_3151;HMR_3422" "RCR12651;RCR12667" "" 0 "" "RHEA:31195" "HMR_3151;HMR_3422;MAR03422" +"MAR03153" "R04747" "" "R04747M" "r0732" "" "r0732;HMR_3422" "MNXR109092" "HMR_3153;HMR_3422" "RCR12652;RCR12667" "" 0 "RHEA:31205" "RHEA:31203" "HMR_3153;HMR_3422;MAR03422" +"MAR03156" "R04751" "r1450" "" "" "R-HSA-77327" "HMR_3156;r1450;HMR_3422" "MNXR109093" "HMR_3156;HMR_3422" "RCR12653;RCR12667" "" 0 "" "RHEA:31207" "HMR_3156;r1450;MAR02372;HMR_3422;MAR03422" +"MAR03157" "R04749" "" "R04749M" "r0734" "" "r0734;HMR_3422" "MNXR97886" "HMR_3157;HMR_3422" "RCR12654;RCR12667" "" 0 "" "RHEA:30547" "HMR_3157;HMR_3422;MAR03422" +"MAR03158" "R04748" "" "R04748M" "r0733" "R-HSA-77323" "r0733;HMR_3422" "MNXR100543" "HMR_3158;HMR_3422" "RCR12655;RCR12667" "" 0 "" "RHEA:31143" "HMR_3158;HMR_3422;MAR03422" +"MAR03160" "R01177" "" "R01177M" "r0287" "R-HSA-77321" "r0287;HMR_3422" "MNXR95196" "HMR_3160;HMR_3422" "RCR12656;RCR12667" "" 0 "" "RHEA:31111" "HMR_3160;HMR_3422;MAR03422" "MAR03398" "" "HMR_3398" "" "" "" "HMR_3398" "" "HMR_3398" "RCR12657" "" 0 "" "" "HMR_3398" "MAR03406" "" "HMR_3406" "" "" "" "HMR_3406" "" "HMR_3406" "RCR12658" "" 0 "" "" "HMR_3406" "MAR03407" "" "" "" "" "" "HMR_3407" "" "HMR_3407" "RCR12659" "" 0 "" "" "HMR_3407" @@ -2667,7 +2667,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03414" "" "" "" "" "" "HMR_3414" "" "HMR_3414" "RCR12664" "" 0 "" "" "HMR_3414" "MAR03416" "" "" "" "" "" "HMR_3416" "" "HMR_3416" "RCR12665" "" 0 "" "" "HMR_3416" "MAR03421" "" "HMR_3421" "" "" "" "HMR_3421" "" "HMR_3421" "RCR12666" "" 0 "" "" "HMR_3421" -"MAR03422" "" "" "" "" "" "HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "HMR_3422" "MAR03423" "" "HMR_3423" "" "" "" "HMR_3423" "" "HMR_3423" "RCR12668" "" 0 "" "" "HMR_3423" "MAR03424" "" "" "" "" "" "HMR_3424" "" "HMR_3424" "RCR12669" "" 0 "" "" "HMR_3424" "MAR03425" "" "" "" "" "" "HMR_3425" "" "HMR_3425" "RCR12670" "" 0 "" "" "HMR_3425" @@ -2780,9 +2779,9 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03290" "" "" "RE1520M" "" "R-HSA-109342" "RE1520M" "MNXR125225" "HMR_3290" "RCR12775" "" 0 "" "" "HMR_3290" "MAR03292" "" "" "RE1527M" "" "" "RE1527M" "" "HMR_3292" "RCR12776" "" 0 "" "" "HMR_3292" "MAR03293" "" "" "RE1534M" "" "" "RE1534M" "" "HMR_3293" "RCR12777" "" 0 "" "" "HMR_3293" -"MAR03294" "" "" "RE1519M" "" "" "FAOXC101C102m" "" "HMR_3294" "RCR12778" "" 0 "" "" "HMR_3294" +"MAR03294" "" "" "RE1519M" "" "" "FAOXC101C102m;HMR_3422" "" "HMR_3294;HMR_3422" "RCR12778;RCR12667" "" 0 "" "" "HMR_3294;HMR_3422;MAR03422" "MAR03296" "" "" "RE3627M" "" "R-HSA-109343" "HMR_3296" "MNXR124610" "HMR_3296" "RCR12779" "" 0 "" "" "HMR_3296" -"MAR03298" "" "" "RE3628M" "" "R-HSA-109998" "RE3628M;FAOXC101m" "MNXR118942" "HMR_3298" "RCR12780" "" 0 "RHEA:45753" "RHEA:45752" "HMR_3298" +"MAR03298" "" "" "RE3628M" "" "R-HSA-109998" "RE3628M;FAOXC101m;HMR_3422" "MNXR118942" "HMR_3298;HMR_3422" "RCR12780;RCR12667" "" 0 "RHEA:45753" "RHEA:45752" "HMR_3298;HMR_3422;MAR03422" "MAR01174" "" "" "RE3383M" "" "" "RE3383M" "" "HMR_1174" "RCR12781" "" 0 "" "" "HMR_1174" "MAR01175" "" "" "RE3385M" "" "" "RE3385M" "" "HMR_1175" "RCR12782" "" 0 "" "" "HMR_1175" "MAR01176" "" "" "RE3391M" "" "" "RE3391M" "" "HMR_1176" "RCR12783" "" 0 "" "" "HMR_1176" @@ -9228,7 +9227,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04965" "" "EX_tetdece1crn_e" "" "" "" "EX_tetdece1crn[e]" "" "" "" "" 0 "" "" "EX_tetdece1crn[e]" "MAR04967" "" "FAOXC101C8m" "" "" "" "FAOXC101C8m" "" "" "" "" 0 "" "" "FAOXC101C8m" "MAR04968" "" "FAOXC101C8x" "" "" "" "FAOXC101C8x" "" "" "" "" 0 "" "" "FAOXC101C8x" -"MAR04970" "" "FAOXC102C101m" "" "" "" "FAOXC102C101m" "" "" "" "" 0 "" "" "FAOXC102C101m" +"MAR04970" "" "FAOXC102C101m" "" "" "" "FAOXC102C101m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC102C101m;HMR_3422;MAR03422" "MAR04974" "" "FAOXC102C101x" "" "" "" "FAOXC102C101x" "" "" "" "" 0 "" "" "FAOXC102C101x" "MAR04978" "" "FAOXC102C103m" "" "" "" "FAOXC102C103m" "" "" "" "" 0 "" "" "FAOXC102C103m" "MAR04981" "" "FAOXC102C103x" "" "" "" "FAOXC102C103x" "" "" "" "" 0 "" "" "FAOXC102C103x" @@ -9246,8 +9245,8 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05030" "" "FAOXC11C9m" "" "" "" "FAOXC11C9m" "" "" "" "" 0 "" "" "FAOXC11C9m" "MAR05044" "" "FAOXC121C101m" "" "" "" "FAOXC121C101m" "" "" "" "" 0 "" "" "FAOXC121C101m" "MAR05069" "" "FAOXC121C10x" "" "" "" "FAOXC121C10x" "" "" "" "" 0 "" "" "FAOXC121C10x" -"MAR05072" "" "FAOXC122C101m" "" "" "" "FAOXC122C101m" "" "" "" "" 0 "" "" "FAOXC122C101m" -"MAR05075" "" "FAOXC122m" "" "" "" "FAOXC122m" "" "" "" "" 0 "" "" "FAOXC122m" +"MAR05072" "" "FAOXC122C101m" "" "" "" "FAOXC122C101m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC122C101m;HMR_3422;MAR03422" +"MAR05075" "" "FAOXC122m" "" "" "" "FAOXC122m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC122m;HMR_3422;MAR03422" "MAR05081" "" "FAOXC122x" "" "" "" "FAOXC122x" "" "" "" "" 0 "" "" "FAOXC122x" "MAR05083" "" "FAOXC123C102m" "" "" "" "FAOXC123C102m" "" "" "" "" 0 "" "" "FAOXC123C102m" "MAR05086" "" "FAOXC123C102x" "" "" "" "FAOXC123C102x" "" "" "" "" 0 "" "" "FAOXC123C102x" @@ -9265,7 +9264,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05111" "" "FAOXC141C121m" "" "" "" "FAOXC141C121m" "" "" "" "" 0 "" "" "FAOXC141C121m" "MAR05119" "" "FAOXC141C121x" "" "" "" "FAOXC141C121x" "" "" "" "" 0 "" "" "FAOXC141C121x" "MAR05120" "" "FAOXC141C141OHm" "" "" "" "FAOXC141C141OHm" "" "" "" "" 0 "" "" "FAOXC141C141OHm" -"MAR05123" "" "FAOXC142C122m" "" "" "" "FAOXC142C122m" "" "" "" "" 0 "" "" "FAOXC142C122m" +"MAR05123" "" "FAOXC142C122m" "" "" "" "FAOXC142C122m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC142C122m;HMR_3422;MAR03422" "MAR05175" "" "FAOXC142C122x" "" "" "" "FAOXC142C122x" "" "" "" "" 0 "" "" "FAOXC142C122x" "MAR05176" "" "FAOXC142C142OHm" "" "" "" "FAOXC142C142OHm" "" "" "" "" 0 "" "" "FAOXC142C142OHm" "MAR05177" "" "FAOXC143C123m" "" "" "" "FAOXC143C123m" "" "" "" "" 0 "" "" "FAOXC143C123m" @@ -9286,17 +9285,17 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05192" "" "FAOXC162C162OHm" "" "" "" "FAOXC162C162OHm" "" "" "" "" 0 "" "" "FAOXC162C162OHm" "MAR05193" "" "FAOXC163C142x" "" "" "" "FAOXC163C142x" "" "" "" "" 0 "" "" "FAOXC163C142x" "MAR05194" "" "FAOXC163C143m" "" "" "" "FAOXC163C143m" "" "" "" "" 0 "" "" "FAOXC163C143m" -"MAR05195" "" "FAOXC163C164Gm" "" "" "" "FAOXC163C164Gm" "" "" "" "" 0 "" "" "FAOXC163C164Gm" +"MAR05195" "" "FAOXC163C164Gm" "" "" "" "FAOXC163C164Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163C164Gm;HMR_3422;MAR03422" "MAR05196" "" "FAOXC163C164x" "" "" "" "FAOXC163C164x" "" "" "" "" 0 "" "" "FAOXC163C164x" -"MAR05208" "" "FAOXC163GC142m" "" "" "" "FAOXC163GC142m" "" "" "" "" 0 "" "" "FAOXC163GC142m" -"MAR05229" "" "FAOXC163Gm" "" "" "" "FAOXC163Gm" "" "" "" "" 0 "" "" "FAOXC163Gm" +"MAR05208" "" "FAOXC163GC142m" "" "" "" "FAOXC163GC142m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163GC142m;HMR_3422;MAR03422" +"MAR05229" "" "FAOXC163Gm" "" "" "" "FAOXC163Gm;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC163Gm;HMR_3422;MAR03422" "MAR05235" "" "FAOXC163x" "" "" "" "FAOXC163x" "" "" "" "" 0 "" "" "FAOXC163x" "MAR05242" "" "FAOXC164C143m" "" "" "" "FAOXC164C143m" "" "" "" "" 0 "" "" "FAOXC164C143m" "MAR05256" "" "FAOXC164C143x" "" "" "" "FAOXC164C143x" "" "" "" "" 0 "" "" "FAOXC164C143x" "MAR05293" "" "FAOXC164C163x" "" "" "" "FAOXC164C163x" "" "" "" "" 0 "" "" "FAOXC164C163x" "MAR05298" "" "FAOXC164C165m" "" "" "" "FAOXC164C165m" "" "" "" "" 0 "" "" "FAOXC164C165m" "MAR05300" "" "FAOXC164C165x" "" "" "" "FAOXC164C165x" "" "" "" "" 0 "" "" "FAOXC164C165x" -"MAR05302" "" "FAOXC164GC163m" "" "" "" "FAOXC164GC163m" "" "" "" "" 0 "" "" "FAOXC164GC163m" +"MAR05302" "" "FAOXC164GC163m" "" "" "" "FAOXC164GC163m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC164GC163m;HMR_3422;MAR03422" "MAR05306" "" "FAOXC164m" "" "" "" "FAOXC164m" "" "" "" "" 0 "" "" "FAOXC164m" "MAR05309" "" "FAOXC164x" "" "" "" "FAOXC164x" "" "" "" "" 0 "" "" "FAOXC164x" "MAR05312" "" "FAOXC165C164m" "" "" "" "FAOXC165C164m" "" "" "" "" 0 "" "" "FAOXC165C164m" @@ -9315,29 +9314,29 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR05357" "" "FAOXC182C182OHm" "" "" "" "FAOXC182C182OHm" "" "" "" "" 0 "" "" "FAOXC182C182OHm" "MAR05358" "" "FAOXC183C163Gm" "" "" "" "FAOXC183C163Gm" "" "" "" "" 0 "" "" "FAOXC183C163Gm" "MAR05359" "" "FAOXC183C163m" "" "" "" "FAOXC183C163m" "" "" "" "" 0 "" "" "FAOXC183C163m" -"MAR05360" "" "FAOXC184C163m" "" "" "" "FAOXC184C163m" "" "" "" "" 0 "" "" "FAOXC184C163m" +"MAR05360" "" "FAOXC184C163m" "" "" "" "FAOXC184C163m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC184C163m;HMR_3422;MAR03422" "MAR05364" "" "FAOXC184C163x" "" "" "" "FAOXC184C163x" "" "" "" "" 0 "" "" "FAOXC184C163x" "MAR05365" "" "FAOXC184C164m" "" "" "" "FAOXC184C164m" "" "" "" "" 0 "" "" "FAOXC184C164m" "MAR05366" "" "FAOXC184C164x" "" "" "" "FAOXC184C164x" "" "" "" "" 0 "" "" "FAOXC184C164x" -"MAR05367" "" "FAOXC184m" "" "" "" "FAOXC184m" "" "" "" "" 0 "" "" "FAOXC184m" +"MAR05367" "" "FAOXC184m" "" "" "" "FAOXC184m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC184m;HMR_3422;MAR03422" "MAR05368" "" "FAOXC184x" "" "" "" "FAOXC184x" "" "" "" "" 0 "" "" "FAOXC184x" "MAR05369" "" "FAOXC185C164m" "" "" "" "FAOXC185C164m" "" "" "" "" 0 "" "" "FAOXC185C164m" "MAR05370" "" "FAOXC185m" "" "" "" "FAOXC185m" "" "" "" "" 0 "" "" "FAOXC185m" "MAR05371" "" "FAOXC18C18OHm" "" "" "" "FAOXC18C18OHm" "" "" "" "" 0 "" "" "FAOXC18C18OHm" "MAR05372" "" "FAOXC201C181x" "" "" "" "FAOXC201C181x" "" "" "" "" 0 "" "" "FAOXC201C181x" -"MAR05373" "" "FAOXC204C184m" "" "" "" "FAOXC204C184m" "" "" "" "" 0 "" "" "FAOXC204C184m" +"MAR05373" "" "FAOXC204C184m" "" "" "" "FAOXC204C184m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC204C184m;HMR_3422;MAR03422" "MAR05374" "" "FAOXC204C205x" "" "" "" "FAOXC204C205x" "" "" "" "" 0 "" "" "FAOXC204C205x" "MAR05375" "" "FAOXC205C184x" "" "" "" "FAOXC205C184x" "" "" "" "" 0 "" "" "FAOXC205C184x" "MAR05376" "" "FAOXC205C185m" "" "" "" "FAOXC205C185m" "" "" "" "" 0 "" "" "FAOXC205C185m" "MAR05377" "" "FAOXC221C201x" "" "" "" "FAOXC221C201x" "" "" "" "" 0 "" "" "FAOXC221C201x" -"MAR05378" "" "FAOXC225C204m" "" "" "" "FAOXC225C204m" "" "" "" "" 0 "" "" "FAOXC225C204m" +"MAR05378" "" "FAOXC225C204m" "" "" "" "FAOXC225C204m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC225C204m;HMR_3422;MAR03422" "MAR05379" "" "FAOXC225C204x" "" "" "" "FAOXC225C204x" "" "" "" "" 0 "" "" "FAOXC225C204x" -"MAR05380" "" "FAOXC225C226m" "" "" "" "FAOXC225C226m" "" "" "" "" 0 "" "" "FAOXC225C226m" +"MAR05380" "" "FAOXC225C226m" "" "" "" "FAOXC225C226m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC225C226m;HMR_3422;MAR03422" "MAR05382" "" "FAOXC225C226x" "" "" "" "FAOXC225C226x" "" "" "" "" 0 "" "" "FAOXC225C226x" -"MAR05383" "" "FAOXC225m" "" "" "" "FAOXC225m" "" "" "" "" 0 "" "" "FAOXC225m" +"MAR05383" "" "FAOXC225m" "" "" "" "FAOXC225m;HMR_3422" "HMR_3422" "" "RCR12667" "" 0 "" "" "FAOXC225m;HMR_3422;MAR03422" "MAR05402" "" "FAOXC225x" "" "" "" "FAOXC225x" "" "" "" "" 0 "" "" "FAOXC225x" "MAR05403" "" "FAOXC226C205m" "" "" "" "FAOXC226C205m" "" "" "" "" 0 "" "" "FAOXC226C205m" -"MAR05404" "" "FAOXC226C225m" "" "" "" "FAOXC226C225m" "" "" "" "" 0 "" "" "FAOXC226C225m" +"MAR05404" "" "FAOXC226C225m" "" "" "" "FAOXC226C225m;HMR_3422" "" "HMR_3422" "RCR12667" "" 0 "" "" "FAOXC226C225m;HMR_3422;MAR03422" "MAR05405" "" "FAOXC226C225x" "" "" "" "FAOXC226C225x" "" "" "" "" 0 "" "" "FAOXC226C225x" "MAR05408" "" "FAOXC226C227m" "" "" "" "FAOXC226C227m" "" "" "" "" 0 "" "" "FAOXC226C227m" "MAR05410" "" "FAOXC226m" "" "" "" "FAOXC226m" "" "" "" "" 0 "" "" "FAOXC226m" From 2787b2c51e8e75e2f5ec45668b5882e584dde16c Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Sun, 10 Dec 2023 17:54:30 -0500 Subject: [PATCH 3/3] fix: GPRs for MAR03269 and MAR03380 --- 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 e7aec4fe..4acfd1da 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -231995,7 +231995,7 @@ - MAM03334m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072506 or ENSG00000084754 or ENSG00000113790 or ENSG00000133835 or ENSG00000138029 or ENSG00000138796" + - gene_reaction_rule: "ENSG00000084754 or ENSG00000072506" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.1.1.35" @@ -232470,7 +232470,7 @@ - MAM03351m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072506 or ENSG00000113790 or ENSG00000133835 or ENSG00000138796" + - gene_reaction_rule: "ENSG00000084754 or ENSG00000072506" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.1.1.35"