PoC: Pipeline for retrieving rules for a given organism

[guillecg]

• [x] Select organism with sequenced genome
• [x] Retrieve EC numbers from DBs:
  • [x] ~BioCyc~ (paid account required)
  • [x] KEGG (via bioservices)
• [x] Query RetroRules for the given EC to create the rules.csv file
  • [x] Done by downloading the RetroRules pre-parsed reaction rule CSV file and merging previous data on EC numbers

[guillecg]

• BRENDA has limited but manually curated information.
• EMBL-EBI's Enzyme Portal is a secondary information resource, so data retrieved must be used carefully.
• ExPASY's ENZYME service cannot be queried by organism AFAIK.

[guillecg]

Closed as per 1eb07c5