Request BIGG reaction
request_bigg_universal_reaction(
url = "http://bigg.ucsd.edu/api/v2/universal/reactions",
reaction_id = "ADA",
return_form = c("list", "data.frame")
)url http://bigg.ucsd.edu/api/v2/universal/reactions
reaction_id, for example, ADA
data.frame or list.
universal metabolite information
x <- request_bigg_universal_reaction(reaction_id = "ADA", return_form = "list")
x
#> $models_containing_reaction
#> bigg_id
#> 1 iAB_RBC_283
#> 2 iAF1260
#> 3 iAF1260b
#> 4 iAM_Pb448
#> 5 iAM_Pc455
#> 6 iAM_Pf480
#> 7 iAM_Pk459
#> 8 iAM_Pv461
#> 9 iAPECO1_1312
#> 10 iAT_PLT_636
#> 11 iB21_1397
#> 12 iBWG_1329
#> 13 ic_1306
#> 14 iCHOv1
#> 15 iCHOv1_DG44
#> 16 iCN718
#> 17 iCN900
#> 18 iE2348C_1286
#> 19 iEC042_1314
#> 20 iEC1344_C
#> 21 iEC1349_Crooks
#> 22 iEC1356_Bl21DE3
#> 23 iEC1364_W
#> 24 iEC1368_DH5a
#> 25 iEC1372_W3110
#> 26 iEC55989_1330
#> 27 iECABU_c1320
#> 28 iECB_1328
#> 29 iECBD_1354
#> 30 iECD_1391
#> 31 iECDH10B_1368
#> 32 iEcDH1_1363
#> 33 iECDH1ME8569_1439
#> 34 iEcE24377_1341
#> 35 iECED1_1282
#> 36 iECH74115_1262
#> 37 iEcHS_1320
#> 38 iECIAI1_1343
#> 39 iECIAI39_1322
#> 40 iECNA114_1301
#> 41 iECO103_1326
#> 42 iECO111_1330
#> 43 iECO26_1355
#> 44 iECOK1_1307
#> 45 iEcolC_1368
#> 46 iECP_1309
#> 47 iECs_1301
#> 48 iECS88_1305
#> 49 iECSE_1348
#> 50 iECSF_1327
#> 51 iEcSMS35_1347
#> 52 iECSP_1301
#> 53 iECUMN_1333
#> 54 iECW_1372
#> 55 iEK1008
#> 56 iEKO11_1354
#> 57 iETEC_1333
#> 58 iG2583_1286
#> 59 iHN637
#> 60 iJN1463
#> 61 iJN746
#> 62 iJO1366
#> 63 iJR904
#> 64 iLB1027_lipid
#> 65 iLF82_1304
#> 66 iLJ478
#> 67 iML1515
#> 68 iMM1415
#> 69 iMM904
#> 70 iND750
#> 71 iNF517
#> 72 iNJ661
#> 73 iNRG857_1313
#> 74 iRC1080
#> 75 iS_1188
#> 76 iSbBS512_1146
#> 77 iSBO_1134
#> 78 iSDY_1059
#> 79 iSF_1195
#> 80 iSFV_1184
#> 81 iSFxv_1172
#> 82 iSSON_1240
#> 83 iUMN146_1321
#> 84 iUMNK88_1353
#> 85 iUTI89_1310
#> 86 iWFL_1372
#> 87 iY75_1357
#> 88 iYL1228
#> 89 iYS1720
#> 90 iYS854
#> 91 iZ_1308
#> 92 RECON1
#> 93 Recon3D
#> 94 STM_v1_0
#> organism
#> 1 Homo sapiens
#> 2 Escherichia coli str. K-12 substr. MG1655
#> 3 Escherichia coli str. K-12 substr. MG1655
#> 4 Plasmodium berghei
#> 5 Plasmodium cynomolgi strain B
#> 6 Plasmodium falciparum 3D7
#> 7 Plasmodium knowlesi strain H
#> 8 Plasmodium vivax Sal-1
#> 9 Escherichia coli APEC O1
#> 10 Homo sapiens
#> 11 Escherichia coli BL21(DE3)
#> 12 Escherichia coli BW2952
#> 13 Escherichia coli CFT073
#> 14 Cricetulus griseus
#> 15 Cricetulus griseus
#> 16 Acinetobacter baumannii AYE
#> 17 Clostridioides difficile 630
#> 18 Escherichia coli O127:H6 str. E2348/69
#> 19 Escherichia coli 042
#> 20 Escherichia coli C
#> 21 Escherichia coli ATCC 8739
#> 22 Escherichia coli BL21(DE3)
#> 23 Escherichia coli W
#> 24 Escherichia coli DH5[alpha]
#> 25 Escherichia coli str. K-12 substr. W3110
#> 26 Escherichia coli 55989
#> 27 Escherichia coli ABU 83972
#> 28 Escherichia coli B str. REL606
#> 29 Escherichia coli 'BL21-Gold(DE3)pLysS AG'
#> 30 Escherichia coli BL21(DE3)
#> 31 Escherichia coli str. K-12 substr. DH10B
#> 32 Escherichia coli DH1
#> 33 Escherichia coli DH1
#> 34 Escherichia coli O139:H28 str. E24377A
#> 35 Escherichia coli ED1a
#> 36 Escherichia coli O157:H7 str. EC4115
#> 37 Escherichia coli HS
#> 38 Escherichia coli IAI1
#> 39 Escherichia coli IAI39
#> 40 Escherichia coli NA114
#> 41 Escherichia coli O103:H2 str. 12009
#> 42 Escherichia coli O111:H- str. 11128
#> 43 Escherichia coli O26:H11 str. 11368
#> 44 Escherichia coli IHE3034
#> 45 Escherichia coli ATCC 8739
#> 46 Escherichia coli 536
#> 47 Escherichia coli O157:H7 str. Sakai
#> 48 Escherichia coli S88
#> 49 Escherichia coli SE11
#> 50 Escherichia coli SE15
#> 51 Escherichia coli SMS-3-5
#> 52 Escherichia coli O157:H7 str. TW14359
#> 53 Escherichia coli UMN026
#> 54 Escherichia coli W
#> 55 Mycobacterium tuberculosis H37Rv
#> 56 Escherichia coli KO11FL
#> 57 Escherichia coli ETEC H10407
#> 58 Escherichia coli O55:H7 str. CB9615
#> 59 Clostridium ljungdahlii DSM 13528
#> 60 Pseudomonas putida KT2440
#> 61 Pseudomonas putida KT2440
#> 62 Escherichia coli str. K-12 substr. MG1655
#> 63 Escherichia coli str. K-12 substr. MG1655
#> 64 Phaeodactylum tricornutum CCAP 1055/1
#> 65 Escherichia coli LF82
#> 66 Thermotoga maritima MSB8
#> 67 Escherichia coli str. K-12 substr. MG1655
#> 68 Mus musculus
#> 69 Saccharomyces cerevisiae S288C
#> 70 Saccharomyces cerevisiae S288C
#> 71 Lactococcus lactis subsp. cremoris MG1363
#> 72 Mycobacterium tuberculosis H37Rv
#> 73 Escherichia coli O83:H1 str. NRG 857C
#> 74 Chlamydomonas reinhardtii
#> 75 Shigella flexneri 2a str. 2457T
#> 76 Shigella boydii CDC 3083-94
#> 77 Shigella boydii Sb227
#> 78 Shigella dysenteriae Sd197
#> 79 Shigella flexneri 2a str. 301
#> 80 Shigella flexneri 5 str. 8401
#> 81 Shigella flexneri 2002017
#> 82 Shigella sonnei Ss046
#> 83 Escherichia coli UM146
#> 84 Escherichia coli UMNK88
#> 85 Escherichia coli UTI89
#> 86 Escherichia coli W
#> 87 Escherichia coli str. K-12 substr. W3110
#> 88 Klebsiella pneumoniae subsp. pneumoniae MGH 78578
#> 89 Salmonella pan-reactome
#> 90 Staphylococcus aureus subsp. aureus USA300_TCH1516
#> 91 Escherichia coli O157:H7 str. EDL933
#> 92 Homo sapiens
#> 93 Homo sapiens
#> 94 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
#>
#> $bigg_id
#> [1] "ADA"
#>
#> $old_identifiers
#> [1] "ADA{}ADNDA{}ADNDA_c"
#>
#> $pseudoreaction
#> [1] "false"
#>
#> $name
#> [1] "Adenosine deaminase"
#>
#> $reaction_string
#> [1] "adn_c + h_c + h2o_c ⇌ ins_c + nh4_c"
#>
#> $metabolites
#> bigg_id name compartment_bigg_id stoichiometry
#> 1 adn Adenosine c -1.0
#> 2 h H+ c -1.0
#> 3 h2o H2O H2O c -1.0
#> 4 ins Inosine c 1.0
#> 5 nh4 Ammonium c 1.0
#>
#> $database_link
#> database
#> 1 RHEA
#> 2 KEGG Reaction
#> 3 BioCyc
#> 4 Reactome Reaction
#> 5 EC Number
#> 6 SEED Reaction
#> 7 MetaNetX (MNX) Equation
#> id
#> 1 24408{}24409{}24410{}24411
#> 2 R01560
#> 3 META:ADENODEAMIN-RXN
#> 4 R-BTA-5693346{}R-CFA-5693346{}R-DDI-5693346{}R-DME-5693346{}R-DRE-5693346{}R-GGA-5693346{}R-HSA-5693346{}R-SSC-5693346{}R-TGU-5693346{}R-XTR-5693346
#> 5 3.5.4.4
#> 6 rxn01137
#> 7 MNXR95432
#>
y <- request_bigg_universal_reaction(reaction_id = "ADA", return_form = "data.frame")
y
#> bigg_id old_identifiers pseudoreaction name
#> 1 ADA ADA{}ADNDA{}ADNDA_c false Adenosine deaminase
#> reaction_string
#> 1 adn_c + h_c + h2o_c ⇌ ins_c + nh4_c
#> models_bigg_id
#> 1 iAB_RBC_283{}iAF1260{}iAF1260b{}iAM_Pb448{}iAM_Pc455{}iAM_Pf480{}iAM_Pk459{}iAM_Pv461{}iAPECO1_1312{}iAT_PLT_636{}iB21_1397{}iBWG_1329{}ic_1306{}iCHOv1{}iCHOv1_DG44{}iCN718{}iCN900{}iE2348C_1286{}iEC042_1314{}iEC1344_C{}iEC1349_Crooks{}iEC1356_Bl21DE3{}iEC1364_W{}iEC1368_DH5a{}iEC1372_W3110{}iEC55989_1330{}iECABU_c1320{}iECB_1328{}iECBD_1354{}iECD_1391{}iECDH10B_1368{}iEcDH1_1363{}iECDH1ME8569_1439{}iEcE24377_1341{}iECED1_1282{}iECH74115_1262{}iEcHS_1320{}iECIAI1_1343{}iECIAI39_1322{}iECNA114_1301{}iECO103_1326{}iECO111_1330{}iECO26_1355{}iECOK1_1307{}iEcolC_1368{}iECP_1309{}iECs_1301{}iECS88_1305{}iECSE_1348{}iECSF_1327{}iEcSMS35_1347{}iECSP_1301{}iECUMN_1333{}iECW_1372{}iEK1008{}iEKO11_1354{}iETEC_1333{}iG2583_1286{}iHN637{}iJN1463{}iJN746{}iJO1366{}iJR904{}iLB1027_lipid{}iLF82_1304{}iLJ478{}iML1515{}iMM1415{}iMM904{}iND750{}iNF517{}iNJ661{}iNRG857_1313{}iRC1080{}iS_1188{}iSbBS512_1146{}iSBO_1134{}iSDY_1059{}iSF_1195{}iSFV_1184{}iSFxv_1172{}iSSON_1240{}iUMN146_1321{}iUMNK88_1353{}iUTI89_1310{}iWFL_1372{}iY75_1357{}iYL1228{}iYS1720{}iYS854{}iZ_1308{}RECON1{}Recon3D{}STM_v1_0
#> models_bigg_organism
#> 1 Homo sapiens{}Escherichia coli str. K-12 substr. MG1655{}Escherichia coli str. K-12 substr. MG1655{}Plasmodium berghei{}Plasmodium cynomolgi strain B{}Plasmodium falciparum 3D7{}Plasmodium knowlesi strain H{}Plasmodium vivax Sal-1{}Escherichia coli APEC O1{}Homo sapiens{}Escherichia coli BL21(DE3){}Escherichia coli BW2952{}Escherichia coli CFT073{}Cricetulus griseus{}Cricetulus griseus{}Acinetobacter baumannii AYE{}Clostridioides difficile 630{}Escherichia coli O127:H6 str. E2348/69{}Escherichia coli 042{}Escherichia coli C{}Escherichia coli ATCC 8739{}Escherichia coli BL21(DE3){}Escherichia coli W{}Escherichia coli DH5[alpha]{}Escherichia coli str. K-12 substr. W3110{}Escherichia coli 55989{}Escherichia coli ABU 83972{}Escherichia coli B str. REL606{}Escherichia coli 'BL21-Gold(DE3)pLysS AG'{}Escherichia coli BL21(DE3){}Escherichia coli str. K-12 substr. DH10B{}Escherichia coli DH1{}Escherichia coli DH1{}Escherichia coli O139:H28 str. E24377A{}Escherichia coli ED1a{}Escherichia coli O157:H7 str. EC4115{}Escherichia coli HS{}Escherichia coli IAI1{}Escherichia coli IAI39{}Escherichia coli NA114{}Escherichia coli O103:H2 str. 12009{}Escherichia coli O111:H- str. 11128{}Escherichia coli O26:H11 str. 11368{}Escherichia coli IHE3034{}Escherichia coli ATCC 8739{}Escherichia coli 536{}Escherichia coli O157:H7 str. Sakai{}Escherichia coli S88{}Escherichia coli SE11{}Escherichia coli SE15{}Escherichia coli SMS-3-5{}Escherichia coli O157:H7 str. TW14359{}Escherichia coli UMN026{}Escherichia coli W{}Mycobacterium tuberculosis H37Rv{}Escherichia coli KO11FL{}Escherichia coli ETEC H10407{}Escherichia coli O55:H7 str. CB9615{}Clostridium ljungdahlii DSM 13528{}Pseudomonas putida KT2440{}Pseudomonas putida KT2440{}Escherichia coli str. K-12 substr. MG1655{}Escherichia coli str. K-12 substr. MG1655{}Phaeodactylum tricornutum CCAP 1055/1{}Escherichia coli LF82{}Thermotoga maritima MSB8{}Escherichia coli str. K-12 substr. MG1655{}Mus musculus{}Saccharomyces cerevisiae S288C{}Saccharomyces cerevisiae S288C{}Lactococcus lactis subsp. cremoris MG1363{}Mycobacterium tuberculosis H37Rv{}Escherichia coli O83:H1 str. NRG 857C{}Chlamydomonas reinhardtii{}Shigella flexneri 2a str. 2457T{}Shigella boydii CDC 3083-94{}Shigella boydii Sb227{}Shigella dysenteriae Sd197{}Shigella flexneri 2a str. 301{}Shigella flexneri 5 str. 8401{}Shigella flexneri 2002017{}Shigella sonnei Ss046{}Escherichia coli UM146{}Escherichia coli UMNK88{}Escherichia coli UTI89{}Escherichia coli W{}Escherichia coli str. K-12 substr. W3110{}Klebsiella pneumoniae subsp. pneumoniae MGH 78578{}Salmonella pan-reactome{}Staphylococcus aureus subsp. aureus USA300_TCH1516{}Escherichia coli O157:H7 str. EDL933{}Homo sapiens{}Homo sapiens{}Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
#> metabolite_bigg_id metabolite_name
#> 1 adn{}h{}h2o{}ins{}nh4 Adenosine{}H+{}H2O H2O{}Inosine{}Ammonium
#> metabolites_compartment_bigg_id metabolites_stoichiometry
#> 1 c{}c{}c{}c{}c -1.0{}-1.0{}-1.0{}1.0{}1.0
#> BioCyc EC_Number KEGG MetaNetX RHEA
#> 1 META:ADENODEAMIN-RXN 3.5.4.4 R01560 MNXR95432 24408{}24409{}24410{}24411
#> Reactome
#> 1 R-BTA-5693346{}R-CFA-5693346{}R-DDI-5693346{}R-DME-5693346{}R-DRE-5693346{}R-GGA-5693346{}R-HSA-5693346{}R-SSC-5693346{}R-TGU-5693346{}R-XTR-5693346
#> SEED
#> 1 rxn01137