Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Remove Duplicate Decanoyl-CoA to Octanoyl-CoA Beta-Oxidation Reactions #789

Merged
merged 4 commits into from
Dec 27, 2023
Merged

Remove Duplicate Decanoyl-CoA to Octanoyl-CoA Beta-Oxidation Reactions #789

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
cc7ad31
fix: remove MAR05019 for being a duplicate of MAR03142+MAR03143
Devlin-Moyer Dec 26, 2023
a5c4cda
fix: remove MAR04967 for being a duplicate of MAR03143+MAR03144+MAR03146
Devlin-Moyer Dec 26, 2023
06ac48b
fix: remove MAR05024 for being a duplicate of MAR03142+MAR03143+MAR03…
Devlin-Moyer Dec 26, 2023
982c5c6
Merge branch 'develop' into fix/decanoyl_beta_ox_dupes
haowang-bioinfo Dec 27, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -276,3 +276,6 @@ 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"
65 changes: 0 additions & 65 deletions model/Human-GEM.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -238974,28 +238974,6 @@
- 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"
Expand Down Expand Up @@ -239206,49 +239184,6 @@
- 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"
Expand Down
11 changes: 4 additions & 7 deletions model/reactions.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2643,10 +2643,10 @@ 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"
Expand Down Expand Up @@ -9218,7 +9218,6 @@ 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"
"MAR04974" "" "FAOXC102C101x" "" "" "" "FAOXC102C101x" "" "" "" "" 0 "" "" "FAOXC102C101x"
Expand All @@ -9230,8 +9229,6 @@ 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"
Expand Down