Web scraping in the KEGG db

Question

[bpvalderrama]

Hi everyone!

I'm doing a project on 16S data and used Piphillin to infer functional capacities. The output was a .txt file with several ID numbers for pathways in the KEGG database. My question is whether there is a way for web scraping the table w/ this information from this website. It could also be a R package or whatever that I could use to automatize the match between de KEGG code and bio-function.

The lab I'm working with has almost 0 bioinformatic training and they do the identification by looking -manually- for each code and then write the biological significance in an excel file.

Thanks for your answers :)

[GenoMax]

You can use answers in:
Extracting List Of Genes Associated With A Pathway In Kegg
R: download all KEGG pathways including KO and Compounds

Be careful about doing bulk downloads. You may violate their acceptable use policy if you try to download the entire database.

[bpvalderrama]

For people that could also be interested, I found the KEGG API pretty straightforward for that purpose

Answer 1

[svp]

You can try using TOGOWS

get the genes for Alzheimer disease: hsa05010 as JSON

http://togows.dbcls.jp/entry/pathway/hsa05010/genes.json

[
  {
    "102": "ADAM10; ADAM metallopeptidase domain 10 [KO:K06704] [EC:3.4.24.81]",
    "6868": "ADAM17; ADAM metallopeptidase domain 17 [KO:K06059] [EC:3.4.24.86]",
    "351": "APP; amyloid beta precursor protein [KO:K04520]",
    "8883": "NAE1; NEDD8 activating enzyme E1 subunit 1 [KO:K04532]",
    "322": "APBB1; amyloid beta precursor protein binding family B member 1 [KO:K04529]",
    "2597": "GAPDH; glyceraldehyde-3-phosphate dehydrogenase [KO:K00134] [EC:1.2.1.12]",
    "23621": "BACE1; beta-secretase 1 [KO:K04521] [EC:3.4.23.46]",
    "25825": "BACE2; beta-secretase 2 [KO:K07747] [EC:3.4.23.45]",
    "10313": "RTN3; reticulon 3 [KO:K20723]",
    "57142": "RTN4; reticulon 4 [KO:K20720]",
    "55851": "PSENEN; presenilin enhancer, gamma-secretase subunit [KO:K06170]",
    "5663": "PSEN1; presenilin 1 [KO:K04505] [EC:3.4.23.-]",
    "5664": "PSEN2; presenilin 2 [KO:K04522] [EC:3.4.23.-]",
    "23385": "NCSTN; nicastrin [KO:K06171]",
    "51107": "APH1A; aph-1 homolog A, gamma-secretase subunit [KO:K06172]",
    "83464": "APH1B; aph-1 homolog B, gamma-secretase subunit [KO:K06172]",
    "3416": "IDE; insulin degrading enzyme [KO:K01408] [EC:3.4.24.56]",
    "4311": "MME; membrane metalloendopeptidase [KO:K01389] [EC:3.4.24.11]",
    "4137": "MAPT; microtubule associated protein tau [KO:K04380]",
    "4535": "ND1; NADH dehydrogenase, subunit 1 (complex I) [KO:K03878] [EC:7.1.1.2]",
    "4536": "ND2; MTND2 [KO:K03879] [EC:7.1.1.2]",
    "4537": "ND3; NADH dehydrogenase, subunit 3 (complex I) [KO:K03880] [EC:7.1.1.2]",
    "4538": "ND4; NADH dehydrogenase, subunit 4 (complex I) [KO:K03881] [EC:7.1.1.2]",
    "4539": "ND4L; NADH dehydrogenase, subunit 4L (complex I) [KO:K03882] [EC:7.1.1.2]",
    "4540": "ND5; NADH dehydrogenase, subunit 5 (complex I) [KO:K03883] [EC:7.1.1.2]",
    "4541": "ND6; NADH dehydrogenase, subunit 6 (complex I) [KO:K03884] [EC:7.1.1.2]",
    "4723": "NDUFV1; NADH:ubiquinone oxidoreductase core subunit V1 [KO:K03942] [EC:7.1.1.2]",
    "4729": "NDUFV2; NADH:ubiquinone oxidoreductase core subunit V2 [KO:K03943] [EC:7.1.1.2]",
    "4731": "NDUFV3; NADH:ubiquinone oxidoreductase subunit V3 [KO:K03944]",
    "4694": "NDUFA1; NADH:ubiquinone oxidoreductase subunit A1 [KO:K03945]",
    "4695": "NDUFA2; NADH:ubiquinone oxidoreductase subunit A2 [KO:K03946]",
    "4696": "NDUFA3; NADH:ubiquinone oxidoreductase subunit A3 [KO:K03947]",
    "4697": "NDUFA4; NDUFA4 mitochondrial complex associated [KO:K03948]",
    "56901": "NDUFA4L2; NDUFA4 mitochondrial complex associated like 2 [KO:K03948]",
    "4698": "NDUFA5; NADH:ubiquinone oxidoreductase subunit A5 [KO:K03949]",
    "4700": "NDUFA6; NADH:ubiquinone oxidoreductase subunit A6 [KO:K03950]",
    "4701": "NDUFA7; NADH:ubiquinone oxidoreductase subunit A7 [KO:K03951]",
    "4702": "NDUFA8; NADH:ubiquinone oxidoreductase subunit A8 [KO:K03952]",
    "4704": "NDUFA9; NADH:ubiquinone oxidoreductase subunit A9 [KO:K03953]",
    "4705": "NDUFA10; NADH:ubiquinone oxidoreductase subunit A10 [KO:K03954]",
    "4706": "NDUFAB1; NADH:ubiquinone oxidoreductase subunit AB1 [KO:K03955]",
    "126328": "NDUFA11; NADH:ubiquinone oxidoreductase subunit A11 [KO:K03956]",
    "55967": "NDUFA12; NADH:ubiquinone oxidoreductase subunit A12 [KO:K11352]",
    "51079": "NDUFA13; NADH:ubiquinone oxidoreductase subunit A13 [KO:K11353]",
    "4707": "NDUFB1; NADH:ubiquinone oxidoreductase subunit B1 [KO:K03957]",
    "4714": "NDUFB8; NADH:ubiquinone oxidoreductase subunit B8 [KO:K03964]",
    "4715": "NDUFB9; NADH:ubiquinone oxidoreductase subunit B9 [KO:K03965]",
    "4716": "NDUFB10; NADH:ubiquinone oxidoreductase subunit B10 [KO:K03966]",
    "54539": "NDUFB11; NADH:ubiquinone oxidoreductase subunit B11 [KO:K11351]",
    "4719": "NDUFS1; NADH:ubiquinone oxidoreductase core subunit S1 [KO:K03934] [EC:7.1.1.2]",
    "4720": "NDUFS2; NADH:ubiquinone oxidoreductase core subunit S2 [KO:K03935] [EC:7.1.1.2]",
    "4722": "NDUFS3; NADH:ubiquinone oxidoreductase core subunit S3 [KO:K03936] [EC:7.1.1.2]",
    "4724": "NDUFS4; NADH:ubiquinone oxidoreductase subunit S4 [KO:K03937]",
    "4725": "NDUFS5; NADH:ubiquinone oxidoreductase subunit S5 [KO:K03938]",
    "4726": "NDUFS6; NADH:ubiquinone oxidoreductase subunit S6 [KO:K03939]",
    "374291": "NDUFS7; NADH:ubiquinone oxidoreductase core subunit S7 [KO:K03940] [EC:7.1.1.2]",
    "4728": "NDUFS8; NADH:ubiquinone oxidoreductase core subunit S8 [KO:K03941] [EC:7.1.1.2]",

  }
]

Answer 2

[MatthewP]

R package KEGGREST is used to get KEGG pathway data.