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feat: update Rhea ids #506

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merged 8 commits into from
Mar 21, 2023
Merged

feat: update Rhea ids #506

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baa413e
fix: refine NADK GPRs
haowang-bioinfo Mar 17, 2023
6719328
fix-rxn: remove remove MAR04279 from HumanGEM
haowang-bioinfo Mar 19, 2023
334451b
doc: update removed rxn to deprecated identifiers
haowang-bioinfo Mar 19, 2023
c64c632
feat: update Rhea master IDs
haowang-bioinfo Mar 20, 2023
a151b3d
fix: correct Rhea ids for MAR07745
haowang-bioinfo Mar 20, 2023
708c7ee
fix: correct Rhea ids for MAR00478
haowang-bioinfo Mar 20, 2023
1f5dc26
fix: correct Rhea ids for MAR03208
haowang-bioinfo Mar 20, 2023
aa63b30
fix: correct Rhea ids for MAR01589
haowang-bioinfo Mar 20, 2023
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3 changes: 2 additions & 1 deletion data/deprecatedIdentifiers/deprecatedReactions.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -61,4 +61,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR07191" "" "PNTOte" "" "" "" "PNTORDe" "MNXR103051" "" "" "" 0 "" "" "PNTORDe"
"MAR02517" "" "RE0580L" "" "" "" "RE0580L" "MNXR94939" "" "" "" 0 "" "" "RE0580L"
"MAR06710" "" "" "RE2477C" "" "" "RE2477C" "MNXR103685" "HMR_6710" "RCR11403" "" 0 "" "" "HMR_6710"
"MAR06737" "" "" "RE2384C" "" "" "RE2384C" "MNXR103663" "HMR_6737" "RCR14365" "" 0 "" "" "HMR_6737"
"MAR06737" "" "" "RE2384C" "" "" "RE2384C" "MNXR103663" "HMR_6737" "RCR14365" "" 0 "" "" "HMR_6737"
"MAR04279" "R00104" "NADK" "R00104C" "" "" "" "MNXR101882" "HMR_4279" "RCR10008" "" 0 "RHEA:18630" "RHEA:18629" "HMR_4279"
23 changes: 2 additions & 21 deletions model/Human-GEM.yml
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Expand Up @@ -150457,7 +150457,7 @@
- MAM02554m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000008130 or ENSG00000152620"
- gene_reaction_rule: "ENSG00000152620"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.1.23"
Expand All @@ -150476,7 +150476,7 @@
- MAM02554c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000008130 or ENSG00000152620"
- gene_reaction_rule: "ENSG00000008130"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.1.23"
Expand Down Expand Up @@ -150561,25 +150561,6 @@
- subsystem:
- "Nicotinate and nicotinamide metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04279"
- name: "ATP:NAD+ 2'-phosphotransferase"
- metabolites: !!omap
- MAM01285n: 1
- MAM01371n: -1
- MAM02039n: 1
- MAM02552n: -1
- MAM02554n: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000008130 or ENSG00000152620"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.1.23"
- references: "PMID:11594753"
- subsystem:
- "Nicotinate and nicotinamide metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04662"
- name: "Nicotinate D-ribonucleoside:orthophosphate ribosyltransferase"
Expand Down
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