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feat: Add new reactions annotated for genes related to Glycolysis pathway #535
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106e1e4
addRawData for Glycolysis new rxn
feiranl 6e7836a
feat-add code and model change
feiranl 12bac20
fix-confidence score
feiranl 1ee3c2b
fix-the order of the metAnnotation
feiranl ab41b3e
add subsystem and extra annotation for new rxn
feiranl 973081f
feat-update reaction.tsv
feiranl c73db68
fix-bug in the code for metabolite annotation file
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| Original file line number | Diff line number | Diff line change |
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| % This function is for adding new rxns annotated for glycolysis genes of GPRs identified by GPT. | ||
| rxnStruct = importTsvFile('../../data/modelCuration/addRxnGly_20230414.tsv'); | ||
| MetStruct = importTsvFile('../../data/modelCuration/addMetGly_20230414.tsv'); | ||
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| model = importYaml('Human-GEM.yml'); | ||
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| rxnsToAdd.rxns = rxnStruct.rxnID; | ||
| rxnsToAdd.eccodes = rxnStruct.ECNumber; | ||
| rxnsToAdd.equations = rxnStruct.Equation; | ||
| rxnsToAdd.rxnNames = rxnStruct.rxnID; | ||
| rxnsToAdd.lb = zeros(length(rxnStruct.rxnID),1); | ||
| rxnsToAdd.ub = repmat(1000,length(rxnStruct.rxnID),1); | ||
| idx = find(cell2mat(rxnStruct.Reversibility) == 1); | ||
| rxnsToAdd.lb(idx) = -1000; | ||
| rxnsToAdd.grRules = rxnStruct.grRules; | ||
| rxnsToAdd.subSystems = rxnStruct.Subsystems; | ||
| rxnsToAdd.rxnConfidenceScores = zeros(length(rxnStruct.rxnID),1); | ||
| [~,idx] = ismember(MetStruct.MetID,model.mets); | ||
| metsToAdd.mets = MetStruct.MetID(~idx,1); | ||
| metsToAdd.metNames = MetStruct.Name(~idx,1); | ||
| metsToAdd.compartments = MetStruct.Comp(~idx,1); | ||
| metsToAdd.metFormulas = MetStruct.Fromula(~idx,1); | ||
| metsToAdd.metCharges = MetStruct.Charge(~idx,1); | ||
| tmp = []; | ||
| for i = 1:length(metsToAdd.metCharges) | ||
| if ~isempty(metsToAdd.metCharges{i}) | ||
| tmp(i,1) = str2double(metsToAdd.metCharges{i}); | ||
| else | ||
| tmp(i,1) = NaN; | ||
| end | ||
| end | ||
| metsToAdd.metCharges = tmp; | ||
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| [newModel, modelChanges] = addMetabolicNetwork(model,rxnsToAdd,metsToAdd); | ||
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| % export the new mets, new reactions to the table | ||
| structure = importTsvFile('../../model/metabolites.tsv'); | ||
| [~,idx] = ismember(modelChanges.mets.mets,MetStruct.MetID); | ||
| MetStruct.BiGGID(1:length(MetStruct.MetID),1) = {''}; | ||
| % metID metNames metFormulas metCharges compartments metKEGGID metPubChemID metChEBIID metMetaCycID metMetaNetXID | ||
| metNocomp = cellfun(@(s) s(1:8), MetStruct.MetID(idx,1), 'UniformOutput', false); | ||
| structure.mets = [structure.mets;MetStruct.MetID(idx,1)]; | ||
| structure.metBiGGID = [structure.metBiGGID;MetStruct.BiGGID(idx,1)]; | ||
| structure.metKEGGID = [structure.metKEGGID;MetStruct.KEGG(idx,1)]; | ||
| structure.metsNoComp = [structure.metsNoComp;metNocomp]; | ||
| structure.metHMDBID = [structure.metHMDBID;MetStruct.BiGGID(idx,1)]; | ||
| structure.metChEBIID = [structure.metChEBIID;MetStruct.CHEBI(idx,1)]; | ||
| structure.metPubChemID = [structure.metPubChemID;MetStruct.BiGGID(idx,1)]; | ||
| structure.metLipidMapsID = [structure.metLipidMapsID;MetStruct.CHEBI(idx,1)]; | ||
| structure.metEHMNID = [structure.metEHMNID;MetStruct.BiGGID(idx,1)]; | ||
| structure.metHepatoNET1ID = [structure.metHepatoNET1ID;MetStruct.BiGGID(idx,1)]; | ||
| structure.metRecon3DID = [structure.metRecon3DID;MetStruct.BiGGID(idx,1)]; | ||
| structure.metMetaNetXID = [structure.metMetaNetXID;MetStruct.MetaNetx(idx,1)]; | ||
| structure.metHMR2ID = [structure.metHMR2ID;MetStruct.BiGGID(idx,1)]; | ||
| structure.metRetired = [structure.metRetired;MetStruct.BiGGID(idx,1)]; | ||
| % sort the order based on the model.mets | ||
| [~,idx] = ismember(model.mets,structure.mets); | ||
| structure.mets = structure.mets(idx); | ||
| structure.metsNoComp = structure.metsNoComp(idx); | ||
| structure.metBiGGID = structure.metBiGGID(idx,1); | ||
| structure.metKEGGID = structure.metKEGGID(idx,1); | ||
| structure.metHMDBID = structure.metHMDBID(idx,1); | ||
| structure.metChEBIID = structure.metChEBIID(idx,1); | ||
| structure.metPubChemID = structure.metPubChemID(idx,1); | ||
| structure.metLipidMapsID = structure.metLipidMapsID(idx,1); | ||
| structure.metEHMNID = structure.metEHMNID(idx,1); | ||
| structure.metHepatoNET1ID = structure.metHepatoNET1ID(idx,1); | ||
| structure.metRecon3DID = structure.metRecon3DID(idx,1); | ||
| structure.metMetaNetXID = structure.metMetaNetXID(idx,1); | ||
| structure.metHMR2ID = structure.metHMR2ID(idx,1); | ||
| structure.metRetired = structure.metRetired(idx,1); | ||
| exportTsvFile(structure, '../../model/metabolites.tsv') | ||
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| structure = importTsvFile('../../model/reactions.tsv'); | ||
| [~,idx] = ismember(modelChanges.rxns.rxns,rxnStruct.rxnID); | ||
| rxnStruct.EHMN(1:length(rxnStruct.rxnID),1) = {''}; | ||
| structure.rxns = [structure.rxns;rxnStruct.rxnID(idx,1) ]; | ||
| structure.rxnKEGGID = [structure.rxnKEGGID;rxnStruct.KEGG(idx,1) ]; | ||
| structure.rxnBiGGID= [structure.rxnBiGGID;rxnStruct.BiGG(idx,1) ]; | ||
| structure.rxnEHMNID = [structure.rxnEHMNID;rxnStruct.EHMN(idx,1) ]; | ||
| structure.rxnHepatoNET1ID = [structure.rxnHepatoNET1ID;rxnStruct.EHMN(idx,1) ]; | ||
| structure.rxnREACTOMEID = [structure.rxnREACTOMEID;rxnStruct.Reactome(idx,1) ]; | ||
| structure.rxnRecon3DID = [structure.rxnRecon3DID;rxnStruct.EHMN(idx,1) ]; | ||
| structure.rxnMetaNetXID = [structure.rxnMetaNetXID;rxnStruct.MetaNetx(idx,1) ]; | ||
| structure.rxnHMR2ID = [structure.rxnHMR2ID;rxnStruct.EHMN(idx,1) ]; | ||
| structure.rxnRatconID = [structure.rxnRatconID;rxnStruct.EHMN(idx,1) ]; | ||
| structure.rxnTCDBID = [structure.rxnTCDBID;rxnStruct.EHMN(idx,1) ]; | ||
| structure.spontaneous = [structure.spontaneous;zeros(length(rxnStruct.rxnID(idx,1)),1) ]; | ||
| structure.rxnRheaID = [structure.rxnRheaID;rxnStruct.RHEA(idx,1) ]; | ||
| structure.rxnRheaMasterID = [structure.rxnRheaMasterID;rxnStruct.EHMN(idx,1) ]; | ||
| structure.rxnRetired = [structure.rxnRetired;rxnStruct.EHMN(idx,1) ]; | ||
|
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| exportTsvFile(structure, '../../model/reactions.tsv') | ||
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,127 @@ | ||
| MetID Name Fromula Charge Comp KEGG PubChem CHEBI MetaCyc MetaNetx | ||
| MAM02039n H+ H 1 n CHEBI:15378 MNXM1 | ||
| MAM20001n retinol C20H30O n CHEBI:50211 MNXM729111 | ||
| MAM20002n retinal C20H28O 0 n CHEBI:15035 MNXM1105989 | ||
| MAM02552n NAD+ C21H26N7O14P2 n CHEBI:57540 MNXM8 | ||
| MAM02553n NADH C21H27N7O14P2 -2 n CHEBI:57945 MNXM10 | ||
| MAM02039c H+ H 1 c CHEBI:15378 MNXM1 | ||
| MAM02552c NAD+ C21H26N7O14P2 c CHEBI:57540 MNXM8 | ||
| MAM01232n 9-cis-retinol C20H30O 0 n CHEBI:78272 MNXM1102095 | ||
| MAM01230n 9-cis-retinal C20H28O 0 n CHEBI:78273 MNXM1105991 | ||
| MAM20003n 20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate C20H29O3 n CHEBI:76645 MNXM145653 | ||
| MAM20004n (5Z,8Z,11Z,14Z)-eicosatetraenedioate C20H28O4 n CHEBI:76647 MNXM23130 | ||
| MAM20005c 20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate C20H29O3 c CHEBI:76645 MNXM145653 | ||
| MAM20006c (5Z,8Z,11Z,14Z)-eicosatetraenedioate C20H28O4 c CHEBI:76647 MNXM23130 | ||
| MAM00270n 10-HETE C20H31O3 n CHEBI:76624 MNXM732711 | ||
| MAM00270c 10-HETE C20H31O3 c CHEBI:76624 MNXM732711 | ||
| MAM20007n 1,4-benzoquinone C6H4O2 n CHEBI:16509 MNXM740100 | ||
| MAM20008n hydroquinone C6H6O2 n CHEBI:17594 MNXM376 | ||
| MAM20009c 1,4-benzoquinone C6H4O2 c CHEBI:16509 MNXM740100 | ||
| MAM20010c hydroquinone C6H6O2 c CHEBI:17594 MNXM376 | ||
| MAM02833n retinoate C20H27O2 -1 n CHEBI:35291 MNXM1107683 | ||
| MAM02833c retinoate C20H27O2 -1 c CHEBI:35291 MNXM1107683 | ||
| MAM20011m (S)-3-hydroxybutanoate C4H7O3 -1 m CHEBI:11047 MNXM1104966 | ||
| MAM20012m (R)-2-hydroxyglutarate C5H6O5 -2 m CHEBI:15801 MNXM733230 | ||
| MAM01306m AKG C5H4O5 m CHEBI:16810 MNXM20 | ||
| MAM00970c 4-aminobutyrate C4H9NO2 c CHEBI:59888 MNXM192 | ||
| MAM02674c palmitate C16H31O2 -1 c CHEBI:7896 MNXM108 | ||
| MAM20013c octanal C8H16O 0 c CHEBI:17935 MNXM2705 | ||
| MAM02642c octanoic acid C8H15O2 c CHEBI:25646 MNXM750 | ||
| MAM02039g H+ H 1 g CHEBI:15378 MNXM1 | ||
| MAM20014g 15-oxoprostaglandin E2 C20H29O5 g CHEBI:57400 MNXM1619 | ||
| MAM20015g 13,14-dihydro-15-oxo-prostaglandin E2 C20H31O5 g CHEBI:57402 MNXM733372 | ||
| MAM02555g NADPH C21H26N7O17P3 -4 g CHEBI:57783 MNXM738702 | ||
| MAM02554g NADP+ C21H25N7O17P3 g CHEBI:58349 MNXM5 | ||
| MAM20016n 15-oxoprostaglandin E2 C20H29O5 n CHEBI:57400 MNXM1619 | ||
| MAM20017n 13,14-dihydro-15-oxo-prostaglandin E2 C20H31O5 n CHEBI:57402 MNXM733372 | ||
| MAM02554n NADP+ C21H25N7O17P3 n CHEBI:58349 MNXM5 | ||
| MAM02751r Pi HO4P r CHEBI:43474 MNXM9 | ||
| MAM01968r glucose-6-phosphate C6H11O9P -2 r CHEBI:61548 MNXM1105858 | ||
| MAM20018r 19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate C20H33O3 r CHEBI:132024 MNXM163133 | ||
| MAM02039r H+ H 1 r CHEBI:15378 MNXM1 | ||
| MAM20019r FMNH2 C17H21N4O9P -2 r CHEBI:57618 MNXM1107623 | ||
| MAM20020r FMN C17H18N4O9P -3 r CHEBI:58210 MNXM1105928 | ||
| MAM02457r mead acid C20H33O2 r CHEBI:78043 MNXM735122 | ||
| MAM20021i 19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate C20H33O3 i CHEBI:132024 MNXM163133 | ||
| MAM02040i H2O H2O i CHEBI:15377 WATER | ||
| MAM02039i H+ H 1 i CHEBI:15378 MNXM1 | ||
| MAM02630i O2 O2 i CHEBI:15379 MNXM735438 | ||
| MAM20022i FMNH2 C17H21N4O9P -2 i CHEBI:57618 MNXM1107623 | ||
| MAM20023i FMN C17H18N4O9P -3 i CHEBI:58210 MNXM1105928 | ||
| MAM02457i mead acid C20H33O2 i CHEBI:78043 MNXM735122 | ||
| MAM01784r EPA C20H29O2 r CHEBI:58562 MNXM727959 | ||
| MAM20024r 19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate C20H29O3 r CHEBI:76636 MNXM146872 | ||
| MAM01784i EPA C20H29O2 i CHEBI:58562 MNXM727959 | ||
| MAM20025i 19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate C20H29O3 i CHEBI:76636 MNXM146872 | ||
| MAM20026r 21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate C22H31O3 r CHEBI:132025 MNXM35542 | ||
| MAM01689r DHA C22H31O2 r CHEBI:77016 MNXM7161 | ||
| MAM20027i 21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate C22H31O3 i CHEBI:132025 MNXM35542 | ||
| MAM01689i DHA C22H31O2 i CHEBI:77016 MNXM7161 | ||
| MAM02344r lauric acid C12H23O2 r CHEBI:18262 MNXM402 | ||
| MAM20028r 11-hydroxydodecanoate C12H23O3 r CHEBI:76628 MNXM22530 | ||
| MAM02344i lauric acid C12H23O2 i CHEBI:18262 MNXM402 | ||
| MAM20029i 11-hydroxydodecanoate C12H23O3 i CHEBI:76628 MNXM22530 | ||
| MAM20030r 13-hydroxytetradecanoate C14H27O3 r CHEBI:132031 MNXM163120 | ||
| MAM02494r myristic acid C14H27O2 r CHEBI:30807 MNXM314 | ||
| MAM20031i 13-hydroxytetradecanoate C14H27O3 i CHEBI:132031 MNXM163120 | ||
| MAM02494i myristic acid C14H27O2 i CHEBI:30807 MNXM314 | ||
| MAM01019r 4-nitrocatechol C6H4NO4 r CHEBI:57730 MNXM1982 | ||
| MAM02754r PNP C6H4NO3 r CHEBI:57917 MNXM526 | ||
| MAM02554r NADP+ C21H25N7O17P3 r CHEBI:58349 MNXM5 | ||
| MAM01019i 4-nitrocatechol C6H4NO4 i CHEBI:57730 MNXM1982 | ||
| MAM02555i NADPH C21H26N7O17P3 -4 i CHEBI:57783 MNXM738702 | ||
| MAM02754i PNP C6H4NO3 i CHEBI:57917 MNXM526 | ||
| MAM02554i NADP+ C21H25N7O17P3 i CHEBI:58349 MNXM5 | ||
| MAM20032n beta-D-galactose C6H12O6 0 n CHEBI:27667 MNXM112 | ||
| MAM01910n galactose C6H12O6 0 n C00984 439357 CHEBI:28061 MNXM1108175 | ||
| MAM20033c beta-D-galactose C6H12O6 0 c CHEBI:27667 MNXM112 | ||
| MAM01388n beta-D-glucose C6H12O6 0 n CHEBI:15903 MNXM1105026 | ||
| MAM20034n alpha-D-glucose C6H12O6 0 n CHEBI:17925 MNXM1105027 | ||
| MAM20035c alpha-D-glucose C6H12O6 0 c CHEBI:17925 MNXM1105027 | ||
| MAM02554c NADP+ C21H25N7O17P3 c CHEBI:58349 MNXM5 | ||
| MAM20036c benzaldehyde C7H6O c CHEBI:17169 MNXM371 | ||
| MAM20037c hexanal C6H12O c CHEBI:88528 MNXM8718 | ||
| MAM20038c (E)-4-hydroxynon-2-enoate C9H15O3 -1 c CHEBI:142920 MNXM746911 | ||
| MAM20039c (2E)-octenoate C8H13O2 -1 c CHEBI:143526 MNXM1108529 | ||
| MAM20040c (2E)-octenal C8H14O 0 c CHEBI:61748 MNXM1108145 | ||
| MAM01837c formylglutathione C11H16N3O7S c CHEBI:57688 MNXM741595 | ||
| MAM02152c hydroxymethylglutathione C11H18N3O7S c CHEBI:58758 MNXM726277 | ||
| MAM02116r hexadecenal C16H30O r CHEBI:17585 MNXM728262 | ||
| MAM02552r NAD+ C21H26N7O14P2 r CHEBI:57540 MNXM8 | ||
| MAM20041r (E)-hexadec-2-enoate C16H29O2 r CHEBI:72745 MNXM31465 | ||
| MAM02116c hexadecenal C16H30O c CHEBI:17585 MNXM728262 | ||
| MAM20042c (E)-hexadec-2-enoate C16H29O2 c CHEBI:72745 MNXM31465 | ||
| MAM02674r palmitate C16H31O2 -1 r CHEBI:7896 MNXM108 | ||
| MAM20043r 22-oxodocosanoate C22H41O3 r CHEBI:76298 MNXM6762 | ||
| MAM20044c 22-oxodocosanoate C22H41O3 c CHEBI:76298 MNXM6762 | ||
| MAM00564r 2(S)-pristanal C19H38O r CHEBI:49189 MNXM1947 | ||
| MAM02766r pristanic acid C19H37O2 r CHEBI:77268 MNXM3342 | ||
| MAM00564c 2(S)-pristanal C19H38O c CHEBI:49189 MNXM1947 | ||
| MAM02766c pristanic acid C19H37O2 c CHEBI:77268 MNXM3342 | ||
| MAM20045r octadecanal C18H36O r CHEBI:17034 MNXM2269 | ||
| MAM02938r stearate C18H35O2 r CHEBI:25629 MNXM236 | ||
| MAM20046c octadecanal C18H36O c CHEBI:17034 MNXM2269 | ||
| MAM02938c stearate C18H35O2 c CHEBI:25629 MNXM236 | ||
| MAM20047r dodecanal C12H24O 0 r CHEBI:27836 MNXM11432 | ||
| MAM02344c lauric acid C12H23O2 c CHEBI:18262 MNXM402 | ||
| MAM20048c dodecanal C12H24O 0 c CHEBI:27836 MNXM11432 | ||
| MAM01648r decanoic acid C10H19O2 -1 r CHEBI:27689 MNXM1043 | ||
| MAM20049r decanal C10H20O r CHEBI:31457 MNXM7260 | ||
| MAM01648c decanoic acid C10H19O2 -1 c CHEBI:27689 MNXM1043 | ||
| MAM20050c decanal C10H20O c CHEBI:31457 MNXM7260 | ||
| MAM20051r tetradecanal C14H28O r CHEBI:84067 MNXM13002 | ||
| MAM02494c myristic acid C14H27O2 c CHEBI:30807 MNXM314 | ||
| MAM20052c tetradecanal C14H28O c CHEBI:84067 MNXM13002 | ||
| MAM20053r octanal C8H16O 0 r CHEBI:17935 MNXM2705 | ||
| MAM02642r octanoic acid C8H15O2 r CHEBI:25646 MNXM750 | ||
| MAM02108r heptylic acid C7H13O2 r CHEBI:32362 MNXM7416 | ||
| MAM20054r heptanal C7H14O r CHEBI:34787 MNXM8711 | ||
| MAM02108c heptylic acid C7H13O2 c CHEBI:32362 MNXM7416 | ||
| MAM20055c heptanal C7H14O c CHEBI:34787 MNXM8711 | ||
| MAM20056r (2E,6E)-farnesoate C15H23O2 r CHEBI:83276 MNXM735429 | ||
| MAM00677r 2-trans,6-trans-farnesal C15H24O 0 r C03461 CHEBI:15894 MNXM1959 | ||
| MAM20057c (2E,6E)-farnesoate C15H23O2 c CHEBI:83276 MNXM735429 | ||
| MAM20058c all-trans-4-hydroxyretinol C20H30O2 0 c CHEBI:132259 MNXM730551 | ||
| MAM20059c all-trans-4-hydroxyretinal C20H28O2 0 c CHEBI:139346 MNXM166395 | ||
| MAM20060c all-trans-4-oxoretinal C20H26O2 c CHEBI:139347 MNXM745787 | ||
| MAM01032c 4-oxoretinol C20H28O2 c CHEBI:44597 MNXM735096 |
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the line 49 probably should be modified, now ChEBI ids were also updated to the column of Lipidmap ids
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Thanks for identifying this. Changed in the latest commit.