fix: remove MAR03748 and MAR03780 and merge annotations in reactions.…

…tsv into MAR06416/7 and MAR06419/20
SysBioChalmers · Dec 6, 2023 · f554fa2 · f554fa2
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commit f554fa2
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Showing 3 changed files with 7 additions and 46 deletions.
diff --git 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
@@ -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
@@ -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"