From f554fa2021a21fefc2227f02974613af72215a98 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 6 Dec 2023 16:37:49 -0500 Subject: [PATCH] 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"