vignettes/kegg_compound.Rmd
kegg_compound.RmdGet the information of all compounds in KEGG (https://www.genome.jp/kegg/compound/).
library(massdatabase)
compound_info <-
request_kegg_compound_info()
head(compound_info)
#> KEGG.ID
#> 1 C00001
#> 2 C00002
#> 3 C00003
#> 4 C00004
#> 5 C00005
#> 6 C00006
#> Synonyms
#> 1 H2O; Water
#> 2 ATP; Adenosine 5'-triphosphate
#> 3 NAD+; NAD; Nicotinamide adenine dinucleotide; DPN; Diphosphopyridine nucleotide; Nadide; beta-NAD+
#> 4 NADH; DPNH; Reduced nicotinamide adenine dinucleotide
#> 5 NADPH; TPNH; Reduced nicotinamide adenine dinucleotide phosphate
#> 6 NADP+; NADP; Nicotinamide adenine dinucleotide phosphate; beta-Nicotinamide adenine dinucleotide phosphate; TPN; Triphosphopyridine nucleotide; beta-NADP+Get the information of all drugs in KEGG (https://www.genome.jp/kegg/drug/).
drug_info <-
request_kegg_drug_info()
head(drug_info)
#> KEGG.ID
#> 1 D00001
#> 2 D00002
#> 3 D00003
#> 4 D00004
#> 5 D00005
#> 6 D00006
#> Synonyms
#> 1 Water (JP18/USP); Purified water (JP18); Purified water in containers (JP18); Water, purified (USP); Sterile purified water in containers (JP18); Water for injection (JP18); Water for injection in containers (JP18); Sterile water (TN)
#> 2 Nadide (JAN/USAN/INN); Nicotinamide adenine dinucleotide
#> 3 Oxygen (JP18/USP)
#> 4 Carbon dioxide (JP18/USP); Carbon dioxide (TN)
#> 5 Flavin adenine dinucleotide (JAN); Adeflavin (TN)
#> 6 Pyridoxal phosphate hydrate (JP18); Pyridoxal phosphate monohydrate; Hipyridoxin (TN)Get one metabolite information.
x <-
request_kegg_compound(compound_id = "C02886", return_form = "list")
x
#> $ENTRY
#> Compound
#> "C02886"
#>
#> $NAME
#> [1] "S-Hexyl-glutathione;" "S-Hexyl-L-glutathione"
#>
#> $FORMULA
#> [1] "C16H29N3O6S"
#>
#> $EXACT_MASS
#> [1] "391.1777"
#>
#> $MOL_WEIGHT
#> [1] "391.483"
#>
#> $DBLINKS
#> [1] "CAS: 24425-56-7" "PubChem: 5817" "ChEBI: 27704"
#> [4] "PDB-CCD: GTX LEE" "NIKKAJI: J394.269D"
#>
#> $ATOM
#> [1] "26" "1 C6a C 20.4431 -14.8878"
#> [3] "2 O6a O 19.2714 -14.2083" "3 O6a O 20.4493 -16.1764"
#> [5] "4 C1c C 27.4860 -14.8878" "5 C5a C 28.6642 -14.2083"
#> [7] "6 N1b N 26.3143 -14.2083" "7 C1b C 27.5110 -16.4896"
#> [9] "8 O5a O 28.6642 -12.8560" "9 C5a C 25.1363 -14.8878"
#> [11] "10 S2a S 26.2084 -17.2437" "11 C1b C 23.9645 -14.2083"
#> [13] "12 O5a O 25.1363 -16.1764" "13 C1b C 26.2084 -18.6025"
#> [15] "14 C1b C 22.7929 -14.8878" "15 C1b C 25.0367 -19.2818"
#> [17] "16 C1c C 21.6148 -14.2083" "17 C1b C 23.8586 -18.6025"
#> [19] "18 N1a N 21.6148 -12.8560" "19 C1b C 22.6868 -19.2818"
#> [21] "20 C1b C 21.5152 -18.6025" "21 C1a C 20.3371 -19.2818"
#> [23] "22 N1b N 29.8424 -14.9100" "23 C1b C 31.0549 -14.2100"
#> [25] "24 C6a C 32.2673 -14.9100" "25 O6a O 33.4797 -14.2100"
#> [27] "26 O6a O 32.2673 -16.3100"
#>
#> $BOND
#> [1] "25" "1 1 2 1" "2 1 3 2"
#> [4] "3 4 5 1" "4 4 6 1" "5 4 7 1 #Down"
#> [7] "6 5 8 2" "7 6 9 1" "8 7 10 1"
#> [10] "9 9 11 1" "10 9 12 2" "11 10 13 1"
#> [13] "12 11 14 1" "13 13 15 1" "14 14 16 1"
#> [16] "15 15 17 1" "16 16 18 1 #Up" "17 17 19 1"
#> [19] "18 19 20 1" "19 20 21 1" "20 5 22 1"
#> [22] "21 22 23 1" "22 23 24 1" "23 24 25 1"
#> [25] "24 24 26 2" "25 1 16 1"
y <-
request_kegg_compound(compound_id = "C02886", return_form = "data.frame")
y
#> Lab.ID Compound.name Formula mz
#> Compound C02886 S-Hexyl-glutathione{}S-Hexyl-L-glutathione C16H29N3O6S 391.1777
#> CAS.ID HMDB.ID KEGG.ID PUBCHEM.ID CHEBI.ID CHEMBL.ID LIPIDMAPS.ID
#> Compound 24425-56-7 NA C02886 5817 27704 NA NA
#> LIPIDBANK.ID DRUGBANK.ID From_human From_drug KEGG_DRUG.ID
#> Compound NA NA Yes No NA
#> Synonyms
#> Compound S-Hexyl-glutathione{}S-Hexyl-L-glutathioneGet one drug information.
x <-
request_kegg_drug(drug_id = "D00001", return_form = "list")
x
#> $ENTRY
#> Drug
#> "D00001"
#>
#> $NAME
#> [1] "Water (JP18/USP);"
#> [2] "Purified water (JP18);"
#> [3] "Purified water in containers (JP18);"
#> [4] "Water, purified (USP);"
#> [5] "Sterile purified water in containers (JP18);"
#> [6] "Water for injection (JP18);"
#> [7] "Water for injection in containers (JP18);"
#> [8] "Sterile water (TN)"
#>
#> $PRODUCT
#> $PRODUCT$PRODUCT
#> [1] "BACTERIOSTATIC WATER (HF Acquisition Co LLC) 99b0ef9b-600a-40dc-e053-2a95a90aa07e"
#> [2] "BACTERIOSTATIC WATER (Hospira) 87d6e9dc-fe3b-4593-ac9a-d7493d1959c7"
#> [3] "BACTERIOSTATIC WATER (REMEDYREPACK) b8f88bab-c914-4ad2-a096-363d57147948"
#> [4] "STERILE WATER (B. Braun Medical) d99f9133-e4d0-4dee-b611-dbc3f918b547"
#> [5] "STERILE WATER (HF Acquisition Co LLC) 7610bf80-61b7-982f-e053-2a91aa0ac1bb"
#> [6] "STERILE WATER (HF Acquisition Co LLC) 77bd3c0f-f4ab-7cfa-e053-2a91aa0a1b83"
#> [7] "STERILE WATER (HF Acquisition Co LLC) 99b1cb12-0b2d-0c0f-e053-2a95a90ac3b6"
#> [8] "STERILE WATER (HF Acquisition Co. LLC) 74ed2a6f-824c-a1ff-e053-2a91aa0a57c0"
#> [9] "STERILE WATER (A-S Medication Solutions) dba87371-31d2-47c2-ab83-89aabce4b184"
#> [10] "STERILE WATER (Asclemed USA) 45c38269-883c-4198-a9d5-03810a4420ec"
#> [11] "STERILE WATER (B. Braun Medical) 8924e52e-8622-4ed6-a061-1908183e0a18"
#> [12] "STERILE WATER (B. Braun Medical) 8fc8d87a-3951-4ac5-97df-c161ffc90475"
#> [13] "STERILE WATER (B. Braun Medical) f4284eb6-e553-46d4-90d8-efc80a90a480"
#> [14] "STERILE WATER (Baxter Healthcare Company) 210dc9ab-d6ca-4552-ac19-1be17792d290"
#> [15] "STERILE WATER (Baxter Healthcare Company) 8bcf5572-49e1-4302-9522-56f57904cb4a"
#> [16] "STERILE WATER (Baxter Healthcare Corporation) ef3e79c5-3f58-4b36-a296-64b7d9a651c1"
#> [17] "STERILE WATER (Cardinal Health) 9655cd02-82b5-4a75-813b-854b19551481"
#> [18] "BACTERIOSTATIC WATER (General Injectables & Vaccine) 21eadcab-0f74-4d3f-9bcc-6cf7e260fdd0"
#> [19] "STERILE WATER (General Injectables & Vaccines) c6eed2ad-25f3-479e-9c28-1945eea88f8d"
#> [20] "STERILE WATER (General Injectables and Vaccines) a82d2dd5-dd65-4208-ab85-f0680d0e2bf6"
#> [21] "STERILE WATER (Henry Schein) 88403fcf-a276-42c0-88b6-bd84a720b564"
#> [22] "BACTERIOSTATIC WATER (Henry Schein) a833502e-a622-4e81-8c58-cef6ccb6c4c9"
#> [23] "STERILE WATER (Henry Schein) f4087143-9868-4308-b96c-43657ee8ec28"
#> [24] "STERILE WATER (Hospira) 1fe046e2-d6e1-413a-a59c-4ea2a4841c79"
#> [25] "STERILE WATER (Hospira) 2b9ea23a-f9e9-48a8-25b7-519e3bbd6828"
#> [26] "STERILE WATER (ICU Medical) 1c0bbcb7-5ed6-4ee7-b297-080d3359474e"
#> [27] "STERILE WATER (ICU Medical) aab10f03-26ae-4dbc-a481-ef025e48b405"
#> [28] "STERILE WATER (ICU Medical) e3484bc6-ed7f-43ef-9d49-c131a8dff2dd"
#> [29] "BACTERIOSTATIC WATER (Medical Purchasing Solutions) 69485218-9343-952d-e053-2a91aa0ad4e8"
#> [30] "STERILE WATER (Medical Purchasing Solutions) 81a1a49e-fd89-59d8-e053-2a91aa0ac3c3"
#> [31] "STERILE WATER (Medical Purchasing Solutions) 9c9851b6-2702-e893-e053-2a95a90a729c"
#>
#> $PRODUCT$GENERIC
#> [1] "STERILE WATER (Nephron Pharmaceuticals Corporation) bc04a883-babc-87a6-e053-2995a90a3dfd"
#> [2] "STERILE WATER (Medefil) 99e99a50-82d5-aff6-e053-2a95a90a8c56"
#> [3] "STERILE WATER (Civica) 3f49eedf-5bf5-4a95-b704-c956d860ca04"
#> [4] "STERILE WATER (Fresenius Kabi USA) b45e9f1d-9c48-4b46-8541-d846b89540df"
#> [5] "STERILE WATER (Fresenius Kabi USA) e71c6c83-d518-496c-b2ab-efd5987e4783"
#> [6] "STERILE WATER (Hikma Pharmaceuticals USA) 78ef7ad3-451d-43d0-a9b6-5cf0aadca003"
#>
#>
#> $FORMULA
#> [1] "H2O"
#>
#> $EXACT_MASS
#> [1] "18.0106"
#>
#> $MOL_WEIGHT
#> [1] "18.0153"
#>
#> $REMARK
#> [1] "Same as: C00001"
#> [2] "Therapeutic category: 7131"
#> [3] "Product: D00001<JP/US>"
#> [4] "Product (mixture): D05352<JP> D05354<JP> D06417<JP>"
#>
#> $EFFICACY
#> [1] "Pharmaceutic aid (solvent)"
#>
#> $BRITE
#> [1] "Therapeutic category of drugs in Japan [BR:br08301]"
#> [2] " 7 Agents not mainly for therapeutic purpose"
#> [3] " 71 Dispensing medicines"
#> [4] " 713 Solvents"
#> [5] " 7131 Purified water"
#> [6] " D00001 Water (JP18/USP); Purified water (JP18); Purified water in containers (JP18); Water, purified (USP); Sterile purified water in containers (JP18); Water for injection (JP18); Water for injection in containers (JP18)"
#> [7] "Risk category of Japanese OTC drugs [BR:br08312]"
#> [8] " Third-class OTC drugs"
#> [9] " Inorganic and organic chemicals"
#> [10] " Water"
#> [11] " D00001 Water (JP18/USP)"
#> [12] "Drugs listed in the Japanese Pharmacopoeia [BR:br08311]"
#> [13] " Chemicals"
#> [14] " D00001 Water"
#> [15] " D00001 Purified water"
#> [16] " D00001 Purified water in containers"
#> [17] " D00001 Sterile purified Water in containers"
#> [18] " D00001 Water for injection"
#> [19] " D00001 Sterile water for injection in containers"
#>
#> $DBLINKS
#> [1] "CAS: 7732-18-5" "PubChem: 7847069" "ChEBI: 15377"
#> [4] "PDB-CCD: HOH O" "LigandBox: D00001" "NIKKAJI: J43.587B"
#>
#> $ATOM
#> [1] "1" "1 O0 O 32.0259 -17.5852"
#>
#> $BOND
#> [1] "0"
y <-
request_kegg_drug(drug_id = "D00001", return_form = "data.frame")
y
#> Lab.ID
#> Drug D00001
#> Compound.name
#> Drug Water (JP18/USP){}Purified water (JP18){}Purified water in containers (JP18){}Water, purified (USP){}Sterile purified water in containers (JP18){}Water for injection (JP18){}Water for injection in containers (JP18){}Sterile water (TN)
#> Formula mz CAS.ID HMDB.ID KEGG.ID PUBCHEM.ID CHEBI.ID CHEMBL.ID
#> Drug H2O 18.0106 7732-18-5 NA D00001 7847069 15377 NA
#> LIPIDMAPS.ID LIPIDBANK.ID DRUGBANK.ID From_human From_drug KEGG_DRUG.ID
#> Drug NA NA NA Yes Yes
#> Synonyms
#> Drug Water (JP18/USP){}Purified water (JP18){}Purified water in containers (JP18){}Water, purified (USP){}Sterile purified water in containers (JP18){}Water for injection (JP18){}Water for injection in containers (JP18){}Sterile water (TN)
sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur ... 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] massdatabase_0.99.14
#>
#> loaded via a namespace (and not attached):
#> [1] readxl_1.4.0 circlize_0.4.15
#> [3] systemfonts_1.0.4 igraph_1.3.2
#> [5] plyr_1.8.7 lazyeval_0.2.2
#> [7] BiocParallel_1.30.3 listenv_0.8.0
#> [9] ChemmineR_3.48.0 GenomeInfoDb_1.32.2
#> [11] ggplot2_3.3.6 Rdisop_1.56.0
#> [13] digest_0.6.29 foreach_1.5.2
#> [15] yulab.utils_0.0.5 htmltools_0.5.2
#> [17] viridis_0.6.2 massdataset_1.0.5
#> [19] fansi_1.0.3 magrittr_2.0.3
#> [21] memoise_2.0.1 metpath_0.99.4
#> [23] cluster_2.1.3 doParallel_1.0.17
#> [25] tzdb_0.3.0 openxlsx_4.2.5
#> [27] limma_3.52.2 graphlayouts_0.8.0
#> [29] readr_2.1.2 ComplexHeatmap_2.12.0
#> [31] globals_0.15.1 Biostrings_2.64.0
#> [33] matrixStats_0.62.0 pkgdown_2.0.5
#> [35] prettyunits_1.1.1 colorspace_2.0-3
#> [37] ggrepel_0.9.1 rvest_1.0.2
#> [39] metid_1.2.15 textshaping_0.3.6
#> [41] xfun_0.31 dplyr_1.0.9
#> [43] crayon_1.5.1 RCurl_1.98-1.7
#> [45] jsonlite_1.8.0 impute_1.70.0
#> [47] iterators_1.0.14 glue_1.6.2
#> [49] polyclip_1.10-0 gtable_0.3.0
#> [51] zlibbioc_1.42.0 XVector_0.36.0
#> [53] GetoptLong_1.0.5 DelayedArray_0.22.0
#> [55] shape_1.4.6 BiocGenerics_0.42.0
#> [57] scales_1.2.0 vsn_3.64.0
#> [59] DBI_1.1.3 Rcpp_1.0.8.3
#> [61] mzR_2.30.0 progress_1.2.2
#> [63] viridisLite_0.4.0 clue_0.3-61
#> [65] gridGraphics_0.5-1 preprocessCore_1.58.0
#> [67] stats4_4.2.1 MsCoreUtils_1.8.0
#> [69] rsvg_2.3.1 DT_0.23
#> [71] htmlwidgets_1.5.4 httr_1.4.3
#> [73] RColorBrewer_1.1-3 ellipsis_0.3.2
#> [75] farver_2.1.1 pkgconfig_2.0.3
#> [77] XML_3.99-0.10 sass_0.4.1
#> [79] utf8_1.2.2 ggplotify_0.1.0
#> [81] tidyselect_1.1.2 rlang_1.0.3
#> [83] munsell_0.5.0 cellranger_1.1.0
#> [85] tools_4.2.1 cachem_1.0.6
#> [87] cli_3.3.0 generics_0.1.3
#> [89] evaluate_0.15 stringr_1.4.0
#> [91] fastmap_1.1.0 mzID_1.34.0
#> [93] yaml_2.3.5 ragg_1.2.2
#> [95] knitr_1.39 fs_1.5.2
#> [97] tidygraph_1.2.1 zip_2.2.0
#> [99] purrr_0.3.4 ggraph_2.0.5
#> [101] KEGGREST_1.36.2 ncdf4_1.19
#> [103] pbapply_1.5-0 future_1.26.1
#> [105] xml2_1.3.3 compiler_4.2.1
#> [107] rstudioapi_0.13 plotly_4.10.0
#> [109] curl_4.3.2 png_0.1-7
#> [111] affyio_1.66.0 tweenr_1.0.2
#> [113] tibble_3.1.7 bslib_0.3.1
#> [115] stringi_1.7.6 desc_1.4.1
#> [117] MSnbase_2.22.0 lattice_0.20-45
#> [119] ProtGenerics_1.28.0 Matrix_1.4-1
#> [121] ggsci_2.9 vctrs_0.4.1
#> [123] stringdist_0.9.8 pillar_1.7.0
#> [125] lifecycle_1.0.1 furrr_0.3.0
#> [127] BiocManager_1.30.18 jquerylib_0.1.4
#> [129] MALDIquant_1.21 GlobalOptions_0.1.2
#> [131] data.table_1.14.2 bitops_1.0-7
#> [133] GenomicRanges_1.48.0 R6_2.5.1
#> [135] pcaMethods_1.88.0 affy_1.74.0
#> [137] gridExtra_2.3 IRanges_2.30.0
#> [139] parallelly_1.32.0 codetools_0.2-18
#> [141] MASS_7.3-57 assertthat_0.2.1
#> [143] SummarizedExperiment_1.26.1 rprojroot_2.0.3
#> [145] rjson_0.2.21 S4Vectors_0.34.0
#> [147] GenomeInfoDbData_1.2.8 hms_1.1.1
#> [149] parallel_4.2.1 grid_4.2.1
#> [151] tidyr_1.2.0 rmarkdown_2.14
#> [153] MatrixGenerics_1.8.1 masstools_0.99.13
#> [155] ggforce_0.3.3 Biobase_2.56.0
#> [157] base64enc_0.1-3