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Fix Duplicate Stearoyl-CoA Beta-Oxidation Reactions #820

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Fix Duplicate Stearoyl-CoA Beta-Oxidation Reactions #820

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537c89e
fix: removed MAR00776 and MAR00778 from YAML file
Devlin-Moyer May 9, 2024
6dd55fa
feat: added appropriate refs for MAR03115-8 since refs from MAR00776 …
Devlin-Moyer May 9, 2024
afa5828
chore: merged annotations for MAR00776 with those for MAR03115-8 in r…
Devlin-Moyer May 9, 2024
13095fb
chore: merged annotations for MAR00778 with those for MAR03116-MAR031…
Devlin-Moyer May 9, 2024
4b5c411
fix: indentation error in YAML file
Devlin-Moyer May 9, 2024
6e38e73
fix: removed incorrect MetaNetX IDs for MAR03117 and MAR03118
Devlin-Moyer Jun 9, 2024
ea3b478
Merge branch 'develop' into fix/stearoyl-dupes
edkerk Jun 24, 2024
c390e0f
chore: merge in latest develop branch
Devlin-Moyer Oct 17, 2024
3cb489e
chore: add macaw test result
Devlin-Moyer Oct 17, 2024
8f14c55
Merge branch 'develop' into fix/stearoyl-dupes
edkerk Oct 28, 2024
83593b1
chore: add macaw test result
edkerk Oct 28, 2024
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2 changes: 2 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -299,3 +299,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR04205" "" "" "RT0084" "" "" "HMR_4205" "" "HMR_4205" "RCR20258" "" 0 "" "" "HMR_4205"
"MAR08745" "" "THMMPtm" "" "" "" "" "MNXR104822" "HMR_8745" "RCR20669" "" 0 "" "" "HMR_8745"
"MAR08747" "" "THMPPtm" "" "" "" "" "MNXR104824" "HMR_8747" "RCR20670" "" 0 "" "" "HMR_8747"
"MAR00776" "" "FAOXC180" "" "" "" "FAOXC180" "MNXR99313" "" "" "" 0 "" "" "FAOXC180"
"MAR00778" "" "FAOXC1811601m" "" "" "" "FAOXC1811601m" "MNXR99315" "" "" "" 0 "" "" "FAOXC1811601m"
56 changes: 4 additions & 52 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -118350,7 +118350,7 @@
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.3.8.7;1.3.8.8;1.3.8.9;1.3.99.-"
- references: ""
- references: "PMID:20490924"
- subsystem:
- "Beta oxidation of even-chain fatty acids (mitochondrial)"
- confidence_score: 0
Expand All @@ -118367,7 +118367,7 @@
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "4.2.1.17"
- references: ""
- references: "PMID:20490924"
- subsystem:
- "Beta oxidation of even-chain fatty acids (mitochondrial)"
- confidence_score: 0
Expand All @@ -118386,7 +118386,7 @@
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.35;1.1.1.211"
- references: ""
- references: "PMID:20490924"
- subsystem:
- "Beta oxidation of even-chain fatty acids (mitochondrial)"
- confidence_score: 0
Expand All @@ -118404,7 +118404,7 @@
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.3.1.16;1.1.1.211"
- references: ""
- references: "PMID:20490924"
- subsystem:
- "Beta oxidation of even-chain fatty acids (mitochondrial)"
- confidence_score: 0
Expand Down Expand Up @@ -221501,30 +221501,6 @@
- subsystem:
- "Fatty acid oxidation"
- confidence_score: 0
- !!omap
- id: "MAR00776"
- name: "Beta Oxidation of Long Chain Fatty Acid"
- metabolites: !!omap
- MAM01261m: 1
- MAM01597m: -1
- MAM01802m: -1
- MAM01803m: 1
- MAM02039m: 1
- MAM02040m: -1
- MAM02552m: -1
- MAM02553m: 1
- MAM02678m: 1
- MAM02941m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000117054 or ENSG00000122971"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "1.3.99.3"
- references: "PMID:2565344;PMID:3035565"
- subsystem:
- "Fatty acid oxidation"
- confidence_score: 0
- !!omap
- id: "MAR00777"
- name: "Beta Oxidation of Long Chain Fatty Acid"
Expand All @@ -221549,30 +221525,6 @@
- subsystem:
- "Fatty acid oxidation"
- confidence_score: 0
- !!omap
- id: "MAR00778"
- name: "Beta Oxidation Fatty Acid"
- metabolites: !!omap
- MAM00057m: -1
- MAM01261m: 5
- MAM01597m: -5
- MAM01802m: -4
- MAM01803m: 4
- MAM02039m: 5
- MAM02040m: -5
- MAM02552m: -5
- MAM02553m: 5
- MAM02644m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000117054 or ENSG00000122971"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "4.2.1.74"
- references: ""
- subsystem:
- "Fatty acid oxidation"
- confidence_score: 0
- !!omap
- id: "MAR00780"
- name: "Beta Oxidation Fatty Acid"
Expand Down
42 changes: 20 additions & 22 deletions model/reactions.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -2624,26 +2624,26 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR03112" "" "" "" "" "" "HMR_3112" "" "HMR_3112" "RCR12626" "" 0 "" "" "HMR_3112"
"MAR03113" "" "" "" "" "" "HMR_3113" "" "HMR_3113" "RCR12627" "" 0 "" "" "HMR_3113"
"MAR03114" "" "" "" "" "" "HMR_3114" "" "HMR_3114" "RCR12628" "" 0 "" "" "HMR_3114"
"MAR03115" "" "" "" "" "" "HMR_3115" "" "HMR_3115" "RCR12629" "" 0 "" "" "HMR_3115"
"MAR03116" "R07760" "" "" "" "" "HMR_3116" "" "HMR_3116" "RCR12630" "" 0 "RHEA:35349" "RHEA:35347" "HMR_3116"
"MAR03117" "" "" "" "" "" "HMR_3117" "" "HMR_3117" "RCR12631" "" 0 "RHEA:35276" "RHEA:35275" "HMR_3117"
"MAR03118" "" "" "" "" "" "HMR_3118" "" "HMR_3118" "RCR12632" "" 0 "" "" "HMR_3118"
"MAR03121" "R01279" "r0310" "" "" "R-HSA-77299" "HMR_3121;r0310" "MNXR125070" "HMR_3121" "RCR12633" "" 0 "" "RHEA:30747" "HMR_3121;r0310;MAR02035"
"MAR03122" "R04738" "" "R04738X" "r0716" "" "r0716" "MNXR105372;MNXR97892" "HMR_3122" "RCR12634" "" 0 "" "RHEA:31163" "HMR_3122"
"MAR03123" "R04737" "" "R04737X" "r0714" "" "r0714" "MNXR100548;MNXR105371" "HMR_3123" "RCR12635" "" 0 "" "RHEA:31159" "HMR_3123"
"MAR03125" "R03991" "" "R03991X" "r0653" "" "r0653" "MNXR95203" "HMR_3125" "RCR12636" "" 0 "" "RHEA:18161" "HMR_3125"
"MAR03128" "R03990" "r1449" "" "" "R-HSA-77274" "HMR_3128;r1449" "MNXR95300" "HMR_3128" "RCR12637" "" 0 "" "RHEA:28358" "HMR_3128;r1449;MAR02370"
"MAR03129" "R04740" "" "R04740X" "r0720" "" "r0720" "MNXR105373;MNXR97891" "HMR_3129" "RCR12638" "" 0 "" "RHEA:31171" "HMR_3129"
"MAR03130" "R04739" "" "R04739X" "r0718" "" "r0718" "MNXR100547" "HMR_3130" "RCR12639" "" 0 "" "RHEA:31167" "HMR_3130"
"MAR03132" "R03858" "" "R03858X" "r0639" "" "r0639" "MNXR95201" "HMR_3132" "RCR12640" "" 0 "" "RHEA:31091" "HMR_3132"
"MAR03135" "R03857" "r1447" "" "" "R-HSA-77263" "HMR_3135;r1447" "MNXR95299" "HMR_3135" "RCR12641" "" 0 "" "RHEA:31039" "HMR_3135;r1447;MAR02367"
"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;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"
"MAR03115" "" "FAOXC180" "" "" "" "HMR_3115;FAOXC180" "" "HMR_3115" "RCR12629" "" 0 "" "" "HMR_3115;FAOXC180;MAR00776"
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"MAR03116" "R07760" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3116;FAOXC180;FAOXC1811601m" "" "HMR_3116" "RCR12630" "" 0 "RHEA:35349" "RHEA:35347" "HMR_3116;FAOXC180;MAR00776;FAOXC1811601m;MAR00778"
"MAR03117" "" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3117;FAOXC180;FAOXC1811601m" "MNXR99313" "HMR_3117" "RCR12631" "" 0 "RHEA:35276" "RHEA:35275" "HMR_3117;FAOXC180;MAR00776;FAOXC1811601m;MAR00778"
"MAR03118" "" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3118;FAOXC180;FAOXC1811601m" "MNXR99313" "HMR_3118" "RCR12632" "" 0 "" "" "HMR_3118;FAOXC180;MAR00776;FAOXC1811601m;MAR00778"
"MAR03121" "R01279" "r0310;FAOXC1811601m" "" "" "R-HSA-77299" "HMR_3121;r0310;FAOXC1811601m" "MNXR125070" "HMR_3121" "RCR12633" "" 0 "" "RHEA:30747" "HMR_3121;r0310;MAR02035;FAOXC1811601m;MAR00778"
"MAR03122" "R04738" "FAOXC1811601m" "R04738X" "r0716" "" "r0716;FAOXC1811601m" "MNXR105372;MNXR97892" "HMR_3122" "RCR12634" "" 0 "" "RHEA:31163" "HMR_3122;FAOXC1811601m;MAR00778"
"MAR03123" "R04737" "FAOXC1811601m" "R04737X" "r0714" "" "r0714;FAOXC1811601m" "MNXR100548;MNXR105371" "HMR_3123" "RCR12635" "" 0 "" "RHEA:31159" "HMR_3123;FAOXC1811601m;MAR00778"
"MAR03125" "R03991" "FAOXC1811601m" "R03991X" "r0653" "" "r0653;FAOXC1811601m" "MNXR95203" "HMR_3125" "RCR12636" "" 0 "" "RHEA:18161" "HMR_3125;FAOXC1811601m;MAR00778"
"MAR03128" "R03990" "r1449;FAOXC1811601m" "" "" "R-HSA-77274" "HMR_3128;r1449;FAOXC1811601m" "MNXR95300" "HMR_3128" "RCR12637" "" 0 "" "RHEA:28358" "HMR_3128;r1449;MAR02370;FAOXC1811601m;MAR00778"
"MAR03129" "R04740" "FAOXC1811601m" "R04740X" "r0720" "" "r0720;FAOXC1811601m" "MNXR105373;MNXR97891" "HMR_3129" "RCR12638" "" 0 "" "RHEA:31171" "HMR_3129;FAOXC1811601m;MAR00778"
"MAR03130" "R04739" "FAOXC1811601m" "R04739X" "r0718" "" "r0718;FAOXC1811601m" "MNXR100547" "HMR_3130" "RCR12639" "" 0 "" "RHEA:31167" "HMR_3130;FAOXC1811601m;MAR00778"
"MAR03132" "R03858" "FAOXC1811601m" "R03858X" "r0639" "" "r0639;FAOXC1811601m" "MNXR95201" "HMR_3132" "RCR12640" "" 0 "" "RHEA:31091" "HMR_3132;FAOXC1811601m;MAR00778"
"MAR03135" "R03857" "r1447;FAOXC1811601m" "" "" "R-HSA-77263" "HMR_3135;r1447;FAOXC1811601m" "MNXR95299" "HMR_3135" "RCR12641" "" 0 "" "RHEA:31039" "HMR_3135;r1447;MAR02367;FAOXC1811601m;MAR00778"
"MAR03136" "R04170" "r1446;FAOXC1811601m" "R04170X" "r0660" "" "r0660;r1446;FAOXC1811601m" "MNXR97890" "HMR_3136" "RCR12642" "" 0 "" "RHEA:31075" "HMR_3136;r1446;MAR02366;FAOXC1811601m;MAR00778"
"MAR03137" "R04741" "FAOXC1811601m" "R04741X" "r0722" "" "r0722;FAOXC1811601m" "MNXR100546" "HMR_3137" "RCR12643" "" 0 "" "RHEA:31179" "HMR_3137;FAOXC1811601m;MAR00778"
"MAR03139" "R04742" "FAOXC1811601m" "R04742X" "r0724" "" "r0724;FAOXC1811601m" "MNXR95199;MNXR95200" "HMR_3139" "RCR12644" "" 0 "RHEA:31185" "RHEA:31183" "HMR_3139;FAOXC1811601m;MAR00778"
"MAR03142" "R04754" "r1451;FAOXC10C10OHm;FAOXC10080m;FAOXC1811601m" "" "" "R-HSA-77345" "HMR_3142;r1451;FAOXC10C10OHm;FAOXC10C8m;FAOXC1811601m" "MNXR109095" "HMR_3142" "RCR12645" "" 0 "" "RHEA:28354" "HMR_3142;r1451;MAR02373;FAOXC10C10OHm;MAR05019;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778"
"MAR03143" "R04744" "FAOXC10C10OHm;FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R04744X" "r0728" "" "r0728;HMR_3422;FAOXC10C10OHm;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR97889" "HMR_3143;HMR_3422" "RCR12646;RCR12667" "" 0 "" "RHEA:31191" "HMR_3143;HMR_3422;MAR03422;FAOXC10C10OHm;MAR05019;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778"
"MAR03144" "R04743" "FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R04743X" "r0726" "" "r0726;HMR_3422;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR100545" "HMR_3144;HMR_3422" "RCR12647;RCR12667" "" 0 "" "RHEA:31187" "HMR_3144;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778"
"MAR03146" "R03778" "FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R03778X" "r0634" "" "r0634;HMR_3422;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR95198" "HMR_3146;HMR_3422" "RCR12648;RCR12667" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778"
"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"
Expand Down Expand Up @@ -8250,9 +8250,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR00764" "" "FAOXC161802m" "" "" "" "FAOXC161802m" "MNXR99301" "" "" "" 0 "" "" "FAOXC161802m"
"MAR00772" "" "FAOXC16180m" "" "" "" "FAOXC16180m" "MNXR99302" "" "" "" 0 "" "" "FAOXC16180m"
"MAR00774" "" "FAOXC170m" "" "" "" "FAOXC170m" "MNXR99312" "" "" "" 0 "" "" "FAOXC170m"
"MAR00776" "" "FAOXC180" "" "" "" "FAOXC180" "MNXR99313" "" "" "" 0 "" "" "FAOXC180"
"MAR00777" "" "FAOXC180x" "" "" "" "FAOXC180x" "MNXR99314" "" "" "" 0 "" "" "FAOXC180x"
"MAR00778" "" "FAOXC1811601m" "" "" "" "FAOXC1811601m" "MNXR99315" "" "" "" 0 "" "" "FAOXC1811601m"
"MAR00780" "" "FAOXC1811602m" "" "" "" "FAOXC1811602m" "MNXR99316" "" "" "" 0 "" "" "FAOXC1811602m"
"MAR00784" "" "FAOXC1811603m" "" "" "" "FAOXC1811603m" "MNXR99317" "" "" "" 0 "" "" "FAOXC1811603m"
"MAR00785" "" "FAOXC182806m" "" "" "" "FAOXC182806m" "MNXR99321" "" "" "" 0 "" "" "FAOXC182806m"
Expand Down