Merge pull request #789 from SysBioChalmers/fix/decanoyl_beta_ox_dupes

Remove Duplicate Decanoyl-CoA to Octanoyl-CoA Beta-Oxidation Reactions
SysBioChalmers · Dec 27, 2023 · d74abc9 · d74abc9
2 parents 8c10adb + 982c5c6
commit d74abc9
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Showing 3 changed files with 7 additions and 72 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -276,6 +276,9 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR03780"	"R03171"	"OIVD3m"	"R03171M"	"r0602"	""	"OIVD3m"	"MNXR102174;MNXR107999"	"HMR_3780"	"RCR10345"	""	0	""	"RHEA:30907"	"HMR_3780"
 "MAR00789"	""	"FAOXC183803m"	""	""	""	"FAOXC183803m"	"MNXR99325"	""	""	""	0	""	""	"FAOXC183803m"
 "MAR03426"	""	"HMR_3426"	""	""	""	"HMR_3426"	""	"HMR_3426"	"RCR12671"	""	0	""	""	"HMR_3426"
+"MAR05019"	""	"FAOXC10C10OHm"	""	""	""	"FAOXC10C10OHm"	""	""	""	""	0	""	""	"FAOXC10C10OHm"
+"MAR04967"	""	"FAOXC101C8m"	""	""	""	"FAOXC101C8m"	""	""	""	""	0	""	""	"FAOXC101C8m"
+"MAR05024"	""	"FAOXC10080m"	""	""	""	"FAOXC10C8m"	"MNXR99262"	""	""	""	0	""	""	"FAOXC10C8m"
 "MAR03322"	""	""	"RE3627X"	""	""	"HMR_3322"	"MNXR124610"	"HMR_3322"	"RCR14521"	""	0	""	""	"HMR_3322"
 "MAR03296"	""	""	"RE3627M"	""	"R-HSA-109343"	"HMR_3296"	"MNXR124610"	"HMR_3296"	"RCR12779"	""	0	""	""	"HMR_3296"
 "MAR04005"	""	""	""	""	""	"RE3627C"	""	""	""	""	0	""	""	"RE3627C"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -238901,28 +238901,6 @@
       - subsystem:
           - "Exchange/demand reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR04967"
-      - name: "Fatty Acid Beta Oxidation (C10:1->C8), Mitochondrial"
-      - metabolites: !!omap
-          - MAM00039m: -1
-          - MAM01261m: 1
-          - MAM01597m: -1
-          - MAM02039m: 1
-          - MAM02040m: -1
-          - MAM02552m: -1
-          - MAM02553m: 1
-          - MAM02644m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000127884 and ENSG00000138796 and ENSG00000167315"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: "PMID:20195903;PMID:20490924;PMID:17143551"
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
     - !!omap
       - id: "MAR04968"
       - name: "Fatty Acid Beta Oxidation (C10:1->C8:0), Peroxisomal"
@@ -239133,49 +239111,6 @@
       - subsystem:
           - "Fatty acid oxidation"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR05019"
-      - name: "Fatty Acid Beta Oxidation (C10->Ohc10), Mitochondrial"
-      - metabolites: !!omap
-          - MAM00181m: 1
-          - MAM01650m: -1
-          - MAM01802m: -1
-          - MAM01803m: 1
-          - MAM02040m: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000117054 and ENSG00000127884"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: "PMID:1730577;PMID:1912723 ;PMID:7318031"
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR05024"
-      - name: "Fatty Acid Beta Oxidation (C10->C8), Mitochondrial"
-      - metabolites: !!omap
-          - MAM01261m: 1
-          - MAM01597m: -1
-          - MAM01650m: -1
-          - MAM01802m: -1
-          - MAM01803m: 1
-          - MAM02039m: 1
-          - MAM02040m: -1
-          - MAM02552m: -1
-          - MAM02553m: 1
-          - MAM02644m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000117054 and ENSG00000127884 and ENSG00000138796 and ENSG00000167315"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: "PMID:20195903;PMID:20490924;PMID:17143551"
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
     - !!omap
       - id: "MAR05025"
       - name: "Fatty Acid Beta Oxidation (C10->C8), Peroxisomal"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -2642,10 +2642,10 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR03136"	"R04170"	"r1446"	"R04170X"	"r0660"	""	"r0660;r1446"	"MNXR97890"	"HMR_3136"	"RCR12642"	""	0	""	"RHEA:31075"	"HMR_3136;r1446;MAR02366"
 "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;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"
+"MAR03142"	"R04754"	"r1451;FAOXC10C10OHm;FAOXC10080m"	""	""	"R-HSA-77345"	"HMR_3142;r1451;FAOXC10C10OHm;FAOXC10C8m"	"MNXR109095"	"HMR_3142"	"RCR12645"	""	0	""	"RHEA:28354"	"HMR_3142;r1451;MAR02373;FAOXC10C10OHm;MAR05019;FAOXC10C8m;MAR05024"
+"MAR03143"	"R04744"	"FAOXC10C10OHm;FAOXC101C8m;FAOXC10080m"	"R04744X"	"r0728"	""	"r0728;HMR_3422;FAOXC10C10OHm;FAOXC101C8m;FAOXC10C8m"	"MNXR97889"	"HMR_3143;HMR_3422"	"RCR12646;RCR12667"	""	0	""	"RHEA:31191"	"HMR_3143;HMR_3422;MAR03422;FAOXC10C10OHm;MAR05019;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024"
+"MAR03144"	"R04743"	"FAOXC101C8m;FAOXC10080m"	"R04743X"	"r0726"	""	"r0726;HMR_3422;FAOXC101C8m;FAOXC10C8m"	"MNXR100545"	"HMR_3144;HMR_3422"	"RCR12647;RCR12667"	""	0	""	"RHEA:31187"	"HMR_3144;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024"
+"MAR03146"	"R03778"	"FAOXC101C8m;FAOXC10080m"	"R03778X"	"r0634"	""	"r0634;HMR_3422;FAOXC101C8m;FAOXC10C8m"	"MNXR95198"	"HMR_3146;HMR_3422"	"RCR12648;RCR12667"	""	0	"RHEA:31089"	"RHEA:31087"	"HMR_3146;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024"
 "MAR03149"	"R03777"	"r1448;FAOXC8C6m;FAOXC80"	""	""	"R-HSA-77338"	"HMR_3149;r1448;FAOXC6C8m;FAOXC80;HMR_3422"	"MNXR95304"	"HMR_3149;HMR_3422"	"RCR12649;RCR12667"	""	0	""	"RHEA:30943"	"HMR_3149;r1448;MAR02369;FAOXC8C6m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422"
 "MAR03150"	"R04746"	"FAOXC8C6m;FAOXC80"	"R04746M"	"r0731"	""	"r0731;FAOXC8C6m;FAOXC80;HMR_3422"	"MNXR97888"	"HMR_3150;HMR_3422"	"RCR12650;RCR12667"	""	0	""	"RHEA:31199"	"HMR_3150;FAOXC6C8m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422"
 "MAR03151"	"R04745"	"FAOXC8C6m;FAOXC80"	"R04745M"	"r0730"	""	"r0730;FAOXC8C6m;FAOXC80;HMR_3422"	"MNXR100544"	"HMR_3151;HMR_3422"	"RCR12651;RCR12667"	""	0	""	"RHEA:31195"	"HMR_3151;FAOXC8C6m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422"
@@ -9215,7 +9215,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04943"	""	"EX_ivcrn_e"	""	""	""	"EX_ivcrn[e]"	"MNXR98685"	""	""	""	0	""	""	"EX_ivcrn[e]"
 "MAR04950"	""	"EX_tetdec2crn_e"	""	""	""	"EX_tetdec2crn[e]"	""	""	""	""	0	""	""	"EX_tetdec2crn[e]"
 "MAR04965"	""	"EX_tetdece1crn_e"	""	""	""	"EX_tetdece1crn[e]"	""	""	""	""	0	""	""	"EX_tetdece1crn[e]"
-"MAR04967"	""	"FAOXC101C8m"	""	""	""	"FAOXC101C8m"	""	""	""	""	0	""	""	"FAOXC101C8m"
 "MAR04968"	""	"FAOXC101C8x"	""	""	""	"FAOXC101C8x"	""	""	""	""	0	""	""	"FAOXC101C8x"
 "MAR04970"	""	"FAOXC102C101m"	""	""	""	"FAOXC102C101m;HMR_3422"	""	"HMR_3422"	"RCR12667"	""	0	""	""	"FAOXC102C101m;HMR_3422;MAR03422;MAR03296"
 "MAR04974"	""	"FAOXC102C101x"	""	""	""	"FAOXC102C101x"	""	""	""	""	0	""	""	"FAOXC102C101x;MAR03322"
@@ -9227,8 +9226,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04991"	""	"FAOXC102x"	""	""	""	"FAOXC102x"	""	""	""	""	0	""	""	"FAOXC102x"
 "MAR05001"	""	"FAOXC103C102m;HMR_3426"	""	""	""	"FAOXC103C102m;HMR_3426"	""	"HMR_3426"	"RCR12671"	""	0	""	""	"FAOXC103C102m;HMR_3426;MAR03426"
 "MAR05017"	""	"FAOXC103C102x"	""	""	""	"FAOXC103C102x"	""	""	""	""	0	""	""	"FAOXC103C102x"
-"MAR05019"	""	"FAOXC10C10OHm"	""	""	""	"FAOXC10C10OHm"	""	""	""	""	0	""	""	"FAOXC10C10OHm"
-"MAR05024"	""	"FAOXC10080m"	""	""	""	"FAOXC10C8m"	"MNXR99262"	""	""	""	0	""	""	"FAOXC10C8m"
 "MAR05025"	""	"FAOXC10080x"	""	""	""	"FAOXC10C8x"	"MNXR99263"	""	""	""	0	""	""	"FAOXC10C8x"
 "MAR05026"	""	"FAOXC10DCC8DCx"	""	""	""	"FAOXC10DCC8DCx"	""	""	""	""	0	""	""	"FAOXC10DCC8DCx"
 "MAR05028"	""	"FAOXC11BRC9BRx"	""	""	""	"FAOXC11BRC9BRx"	""	""	""	""	0	""	""	"FAOXC11BRC9BRx"