Ecocyc/Biocyc bulk download

Question

[noodle]

Hi biostars,

Is someone aware of how to bulk-download annotation data from ecocyc (biocyc)? For example, I'd like to download an annotation file containing everything in this web-tool; https://www.ecocyc.org/genbro/genbro.shtml?orgid=ECOLI&replicon=COLI-K12

Thanks!

Answer 1

[GenoMax]

Looks like they offer some data for download. Check SmartTables for E.coli data: https://ecocyc.org/groups?tab=PUBLIC&orgid=ECOLI

Also looks like you may need to get a license even for the EcoCyc.

access to the EcoCyc data files is free, although a license is required

There is a warning in their license doc.

Crawling or scraping the Licensed Materials in any form, for any purpose without SRI's prior written consent is expressly prohibited.

[noodle]

Thank you for directing me to these tables, I'm eligible for an academic license and requested one. I'm surprised that there isn't just some 'master' gff that has everything in a neatly formatted heirarchical format, given the amount of work that went into preparing the webpage....

Do you see a table that would have a list of operons, starts/stops/strands, and the genes they cover in the public data? This is what I really need and am unable to find.