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fix: resolve duplicated GCS reactions #538

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merged 8 commits into from
Apr 23, 2023
Merged

fix: resolve duplicated GCS reactions #538

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c679b77
fix-rxn: remove reactions MAR08435, MAR08436, and MAR08437
haowang-bioinfo Apr 20, 2023
6c8e6be
fix-met: remove unused metabolites
haowang-bioinfo Apr 20, 2023
96b9697
fix-rxn: remove low resolution GCS reaction MAR03923
haowang-bioinfo Apr 20, 2023
4093ae8
data: sync removed rxns and mets to deprecated identifiers
haowang-bioinfo Apr 20, 2023
8215f7d
feat: update Rhea ids
haowang-bioinfo Apr 20, 2023
20961d5
fix-gpr: reduce MAR08433 and MAR08434 GPRs to specific components
haowang-bioinfo Apr 21, 2023
3918b12
Merge branch 'develop' into fix/resolveDuplicateGCSreactions
haowang-bioinfo Apr 21, 2023
9168d17
style: reformat PMID
haowang-bioinfo Apr 21, 2023
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3 changes: 3 additions & 0 deletions data/deprecatedIdentifiers/deprecatedMetabolites.tsv
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Expand Up @@ -2191,3 +2191,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM00156c" "MAM00156" "" "" "" "" "53481438" "" "CE2196" "" "CE2196" "MNXM31535" "m00156c" "m00156c"
"MAM02045c" "MAM02045" "" "C09209" "" "CHEBI:5623" "5281404" "" "" "" "C09209" "MNXM11747" "m02045c" "m02045c"
"MAM00077x" "MAM00077" "CE2416" "" "" "" "" "" "CE2416" "" "" "MNXM165274" "m00077p" "m00077p"
"MAM01703m" "MAM01703" "dhlpro" "C02972" "" "CHEBI:16194" "" "" "" "" "dhlpro" "MNXM1663" "m01703m" "m01703m"
"MAM02400m" "MAM02400" "lpro" "C02051" "" "CHEBI:15804" "" "" "" "" "lpro" "MNXM998" "m02400m" "m02400m"
"MAM02879m" "MAM02879" "alpro" "C01242" "" "CHEBI:16882" "" "" "" "" "alpro" "MNXM81221" "m02879m" "m02879m"
4 changes: 4 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -73,3 +73,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR03488" "" "" "RE3073X" "" "" "" "MNXR95747" "HMR_3488" "RCR12589" "" 0 "" "" "HMR_3488"
"MAR03489" "" "" "RE3079X" "" "" "" "" "HMR_3489" "RCR12590" "" 0 "" "" "HMR_3489"
"MAR04456" "R01324" "ACONTm" "R01324C" "r0316" "" "ACONTm" "MNXR95384" "HMR_4456" "RCR10351" "" 0 "" "RHEA:10336" "HMR_4456"
"MAR08435" "R03425" "GCCcm" "" "" "" "GCCam" "MNXR100067;MNXR100069" "HMR_8435" "RCR10246" "" 0 "" "RHEA:24304" "HMR_8435"
"MAR08436" "R04125" "GCHOLAt" "" "" "" "GCCbim" "MNXR100068;MNXR100070" "HMR_8436" "RCR11319" "" 0 "" "RHEA:16945" "HMR_8436"
"MAR08437" "R03815" "GCHOLAt2" "" "" "" "GCCcm" "MNXR100069;MNXR100071" "HMR_8437" "RCR11320" "" 0 "" "" "HMR_8437"
"MAR03923" "R01221" "GLYCLm" "R01221C" "r0295" "" "r0295" "MNXR100330" "HMR_3923" "RCR10962" "" 0 "" "RHEA:27758" "HMR_3923"
112 changes: 4 additions & 108 deletions model/Human-GEM.yml
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Expand Up @@ -23044,14 +23044,6 @@
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM01703m"
- name: "dihydrolipoylprotein"
- compartment: "m"
- formula: "H2S2X"
- charge: 0
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM01704c"
- name: "dihydroneopterin"
Expand Down Expand Up @@ -32860,14 +32852,6 @@
- charge: 0
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02400m"
- name: "lipoylprotein"
- compartment: "m"
- formula: "S2X"
- charge: 0
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02401c"
- name: "L-isoleucyl-tRNA(ile)"
Expand Down Expand Up @@ -39812,14 +39796,6 @@
- charge: 1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02879m"
- name: "S-aminomethyldihydrolipoylprotein"
- compartment: "m"
- formula: "CH6NS2X"
- charge: 1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02880c"
- name: "sarcosine"
Expand Down Expand Up @@ -80493,11 +80469,11 @@
- MAM02878m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
- gene_reaction_rule: "ENSG00000140905 and ENSG00000178445"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.8.1.4;2.1.2.10"
- references: ""
- references: "PMID:24798336"
- subsystem:
- "Glycine, serine and threonine metabolism"
- confidence_score: 0
Expand All @@ -80513,69 +80489,11 @@
- MAM02980m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.8.1.4;2.1.2.10"
- references: ""
- subsystem:
- "Glycine, serine and threonine metabolism"
- confidence_score: 0
- !!omap
- id: "MAR08435"
- name: "glycine:lipoylprotein oxidoreductase (decarboxylating and acceptor-aminomethylating)"
- metabolites: !!omap
- MAM01596m: 1
- MAM01986m: -1
- MAM02039m: -1
- MAM02400m: -1
- MAM02879m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.4.4.2"
- references: ""
- subsystem:
- "Glycine, serine and threonine metabolism"
- confidence_score: 0
- !!omap
- id: "MAR08436"
- name: "[protein]-S8-aminomethyldihydrolipoyllysine:tetrahydrofolate aminomethyltransferase (ammonia-forming)"
- metabolites: !!omap
- MAM01045m: 1
- MAM01703m: 1
- MAM02039m: 1
- MAM02578m: 1
- MAM02879m: -1
- MAM02980m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.8.1.4;2.1.2.10"
- references: ""
- subsystem:
- "Glycine, serine and threonine metabolism"
- confidence_score: 0
- !!omap
- id: "MAR08437"
- name: "dihydrolipoylprotein:NAD+ oxidoreductase"
- metabolites: !!omap
- MAM01703m: 1
- MAM02039m: -1
- MAM02400m: -1
- MAM02552m: 1
- MAM02553m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
- gene_reaction_rule: "ENSG00000140905 and ENSG00000145020"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.8.1.4;2.1.2.10"
- references: ""
- references: "PMID:24798336"
- subsystem:
- "Glycine, serine and threonine metabolism"
- confidence_score: 0
Expand Down Expand Up @@ -153341,28 +153259,6 @@
- subsystem:
- "Inositol phosphate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR03923"
- name: "glycine:NAD+ 2-oxidoreductase (tetrahydrofolate-methylene-adding)"
- metabolites: !!omap
- MAM01045m: 1
- MAM01596m: 1
- MAM01986m: -1
- MAM02039m: 1
- MAM02552m: -1
- MAM02553m: 1
- MAM02578m: 1
- MAM02980m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000091140 and ENSG00000140905 and ENSG00000145020 and ENSG00000178445"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.8.1.4;2.1.2.10"
- references: "PMID:7916605"
- subsystem:
- "Folate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR03925"
- name: "5,6,7,8-tetrahydrobiopterin:NAD+ oxidoreductase"
Expand Down
3 changes: 0 additions & 3 deletions model/metabolites.tsv
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Expand Up @@ -2878,7 +2878,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM01701c" "MAM01701" "dhlam" "C00579" "HMDB0000985" "CHEBI:17694" "663" "" "" "HC00437" "dhlam" "MNXM1277" "m01701c" "m01701c"
"MAM01701m" "MAM01701" "dhlam" "C00579" "HMDB0000985" "CHEBI:17694" "663" "" "" "HC00437" "dhlam" "MNXM1277" "m01701m" "m01701m"
"MAM01702c" "MAM01702" "" "C02147" "HMDB0012210" "CHEBI:18047" "421" "LMFA01130003" "" "" "C02147" "MNXM3585" "m01702c" "m01702c"
"MAM01703m" "MAM01703" "dhlpro" "C02972" "" "CHEBI:16194" "" "" "" "" "dhlpro" "MNXM1663" "m01703m" "m01703m"
"MAM01704c" "MAM01704" "" "C04874" "" "CHEBI:17001" "65074" "" "" "HC01361" "HC01361" "MNXM993" "m01704c" "m01704c"
"MAM01704e" "MAM01704" "" "C04874" "" "CHEBI:17001" "65074" "" "" "HC01361" "HC01361" "MNXM993" "m01704s" "m01704s"
"MAM01705c" "MAM01705" "56dthm" "C00906" "HMDB0000079" "CHEBI:27468" "93556" "" "" "HC00582" "56dthm" "MNXM772" "m01705c" "m01705c"
Expand Down Expand Up @@ -4105,7 +4104,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02397c" "MAM02397" "" "C16239" "" "" "" "" "" "" "M02397" "MNXM19093" "m02397c" "m02397c"
"MAM02398c" "MAM02398" "" "C16238" "" "" "23724672" "" "CE5656" "" "CE5656" "MNXM2392" "m02398c" "m02398c"
"MAM02399c" "MAM02399" "" "" "" "" "53481572" "" "CE2102" "" "CE2102" "MNXM60228" "m02399c" "m02399c"
"MAM02400m" "MAM02400" "lpro" "C02051" "" "CHEBI:15804" "" "" "" "" "lpro" "MNXM998" "m02400m" "m02400m"
"MAM02401c" "MAM02401" "" "C03127" "" "CHEBI:29160" "" "" "" "" "M02401" "MNXM89832" "m02401c" "m02401c"
"MAM02402c" "MAM02402" "" "C03990" "HMDB0000761" "CHEBI:16325" "11740284" "LMST04010003" "" "HC02191" "HC02191" "MNXM886" "m02402c" "m02402c"
"MAM02402x" "MAM02402" "" "C03990" "HMDB0000761" "CHEBI:16325" "11740284" "LMST04010003" "" "HC02191" "HC02191" "MNXM886" "m02402p" "m02402p"
Expand Down Expand Up @@ -4974,7 +4972,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02877n" "MAM02877" "amet" "C00019" "HMDB0001185" "CHEBI:15414" "16757548" "" "" "HC00029" "amet" "MNXM16" "m02877n" "m02877n"
"MAM02877r" "MAM02877" "amet" "C00019" "HMDB0001185" "CHEBI:15414" "16757548" "" "" "HC00029" "amet" "MNXM16" "m02877r" "m02877r"
"MAM02878m" "MAM02878" "alpam" "" "HMDB0006239" "CHEBI:50622" "24906333" "" "" "" "alpam" "MNXM81220" "m02878m" "m02878m"
"MAM02879m" "MAM02879" "alpro" "C01242" "" "CHEBI:16882" "" "" "" "" "alpro" "MNXM81221" "m02879m" "m02879m"
"MAM02880c" "MAM02880" "sarcs" "C00213" "HMDB0000271" "CHEBI:15611" "1088" "" "" "HC00197" "sarcs" "MNXM300" "m02880c" "m02880c"
"MAM02880m" "MAM02880" "sarcs" "C00213" "HMDB0000271" "CHEBI:15611" "1088" "" "" "HC00197" "sarcs" "MNXM300" "m02880m" "m02880m"
"MAM02880x" "MAM02880" "sarcs" "C00213" "HMDB0000271" "CHEBI:15611" "1088" "" "" "HC00197" "sarcs" "MNXM300" "m02880p" "m02880p"
Expand Down
8 changes: 2 additions & 6 deletions model/reactions.tsv
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Expand Up @@ -689,11 +689,8 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR06409" "R01698" "GCC2cm" "R01698C" "r0382" "" "GCC2cm" "MNXR100066" "HMR_6409" "RCR14321" "" 0 "" "RHEA:33059" "HMR_6409"
"MAR07702" "R00465" "" "" "" "" "GLYCLTDy" "MNXR100332" "HMR_7702" "RCR11317" "" 0 "" "RHEA:10992" "HMR_7702"
"MAR07703" "R00475" "" "" "" "" "HMR_7703" "MNXR100338" "HMR_7703" "RCR10524" "" 0 "" "RHEA:25311" "HMR_7703"
"MAR08433" "" "GCC2cm" "" "" "" "GCC2am" "MNXR100066" "HMR_8433" "RCR11318" "" 0 "" "" "HMR_8433"
"MAR08434" "" "GCCam" "" "" "" "GCC2bim" "MNXR100067" "HMR_8434" "RCR14322" "" 0 "" "" "HMR_8434"
"MAR08435" "R03425" "GCCcm" "" "" "" "GCCam" "MNXR100067;MNXR100069" "HMR_8435" "RCR10246" "" 0 "" "RHEA:24304" "HMR_8435"
"MAR08436" "R04125" "GCHOLAt" "" "" "" "GCCbim" "MNXR100068;MNXR100070" "HMR_8436" "RCR11319" "" 0 "" "RHEA:16945" "HMR_8436"
"MAR08437" "R03815" "GCHOLAt2" "" "" "" "GCCcm" "MNXR100069;MNXR100071" "HMR_8437" "RCR11320" "" 0 "" "" "HMR_8437"
"MAR08433" "" "GCC2cm" "" "" "" "GCC2am" "MNXR100066" "HMR_8433" "RCR11318" "" 0 "" "RHEA:24304" "HMR_8433"
"MAR08434" "" "GCCam" "" "" "" "GCC2bim" "MNXR100067" "HMR_8434" "RCR14322" "" 0 "" "RHEA:16945" "HMR_8434"
"MAR08439" "" "DMHPTCRNCPT2" "" "" "" "DMGDHm" "MNXR97521" "HMR_8439" "RCR11321" "" 0 "" "" "HMR_8439"
"MAR08440" "R02565" "BETALDHxm" "" "" "" "BETALDHxm" "MNXR96237" "HMR_8440" "RCR11322" "" 0 "" "RHEA:15305" "HMR_8440"
"MAR08441" "" "CHOLK" "" "" "" "CHOLD2m" "MNXR96702" "HMR_8441" "RCR11323" "" 0 "" "" "HMR_8441"
Expand Down Expand Up @@ -4480,7 +4477,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR08833" "" "PIPLCn" "" "" "" "PIPLCn" "MNXR102851" "HMR_8833" "RCR10417" "" 0 "" "" "HMR_8833"
"MAR08835" "" "PMI1346PH" "" "" "" "PMI1346PH" "MNXR101556" "HMR_8835" "RCR10961" "" 0 "" "" "HMR_8835"
"MAR08836" "" "PMI1346PHn" "" "" "" "PMI1346PHn" "MNXR101556" "HMR_8836" "RCR13801" "" 0 "" "" "HMR_8836"
"MAR03923" "R01221" "GLYCLm" "R01221C" "r0295" "" "r0295" "MNXR100330" "HMR_3923" "RCR10962" "" 0 "" "RHEA:27758" "HMR_3923"
"MAR03925" "R01793" "DHPR" "R01793C" "r0397" "" "DHPR" "MNXR107172;MNXR97436" "HMR_3925" "RCR13802" "" 0 "" "RHEA:32251" "HMR_3925"
"MAR03929" "R02302" "FTCD" "R02302C" "r0524" "" "FORTHFC" "MNXR99667" "HMR_3929" "RCR13803" "" 0 "" "RHEA:22736" "HMR_3929"
"MAR03972" "R09093" "FldAct" "" "" "" "FldAct" "" "HMR_3972" "RCR13804" "" 0 "" "RHEA:68264" "HMR_3972"
Expand Down