https://github.com/gedankenstuecke/kegg-miner

getting data out of KEGG w/o any subscription
https://github.com/gedankenstuecke/kegg-miner

Last synced: about 2 months ago
JSON representation

getting data out of KEGG w/o any subscription

• Host: GitHub
• URL: https://github.com/gedankenstuecke/kegg-miner
• Owner: gedankenstuecke
• License: mit
• Created: 2015-12-17T08:11:23.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2016-01-22T10:20:56.000Z (almost 9 years ago)
• Last Synced: 2024-06-11T16:26:27.992Z (7 months ago)
• Language: Python
• Size: 5.86 KB
• Stars: 3
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# KEGG miner

Unfortunately *KEGG* does not offer free access to their FTP any longer. Instead you would now need a subscription to access the data. If you still would like to access and use their data you could just scrape it from their website. For my own research I was interested in the annotations for all the KEGG genomes (~4000 at this point).

Thankfully the URL structure of their website is pretty simple, so you can easily request those pages automatically. The script *kegg-parsers.py* does just this: It first gets the list of all organisms, then it proceeds to get all gene identifiers and downloads the individual gene html-pages. Those can then be processed using BeautifulSoup as well.

## there could be some fancy political statement here

like, information wants to be free or so, you know.