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I was reading the KEGG plea and I found that it doesn't forbid using the KEGG API. Then, what is in the FTP server license for personal use/academic use that it is not covered by the API?

Or I could download all the database via the API?

PS: I couldn't find how to download which genes are in which pathways but it might be I didn't expend enough time with the queries.

terdon
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llrs
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3 Answers3

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I found the way to download the genes and pathways thanks to this answer using KEGGREST.

It seems that the API allows to fully download the database because it allows to download info, list, find, get, conv, link, ddi.

In fact in the message of 2011-05-21 it mentions that the API includes more options to download the KGML files that previously where only possible to get via the FTP site.

llrs
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If you like to get pathways and corresponding genes as simple table format in a plain text file, use GeneSCF 'prepare_database' module. This can be simple solution.

FTP vs API:

The differences I see is,

  • quick access to the updated content via FTP. With that I assume using FTP version you will have access to weekly database updates. Also bulk download is possible and more convenient via FTP subscription.

  • But KEGG REST API updates once in month or two months or a year (not a recently updated contents).

EagleEye
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  • Thanks for your reply, and welcome to the site! That's the kind of information I use but not what I was asking about. But GeneSCF assumes it can access the whole KEGG database via API. Could you confirm it? – llrs Jun 14 '18 at 14:32
  • It uses KEGG REST (https://www.kegg.jp/kegg/rest/keggapi.html) to access data only for specified organism. It never stores or reterives whole KEGG database. Check out [GeneSCF publication] (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1250-z) for complete details of workflow. – EagleEye Jun 14 '18 at 14:38
  • I've read the relevant parts of it and it didn't answer my question. – llrs Jun 14 '18 at 14:43
  • Sorry if that did not answer your question. I thought I answered "PS: I couldn't find how to download which genes are in which pathways but it might be I didn't expend enough time with the queries." this part. Good luck. – EagleEye Jun 14 '18 at 14:47
  • Oh, that got already answered in the other answer. Thanks, and my apologies – llrs Jun 14 '18 at 14:55
  • So, the API data is not updated at the same time that the FTP files. That's interesting: Is there any written documentation about this to read more about it? – llrs Jun 14 '18 at 15:06
  • You click those links I provided. You will get an idea about what I mentioned. There is no direct statement but if you compare those two pages, that's the information I get. – EagleEye Jun 14 '18 at 15:15
  • I must miss the point, I can only confirm the weekly updated KEGG FTP (on Tuesday JST) , not the update frequency of the KEGG REST API data. Anyway, thanks for your patience (I won't bother you more). – llrs Jun 14 '18 at 15:29
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We implemented Bio2BEL KEGG package to download the KEGG database via its RESTful API

llrs
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ddomingo
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  • Welcome to the site Daniel. Thanks for sharing! I was reading the ComPath article precisely now. But I was not asking if it is possible to download data, but if it is possible to download all the database via the API, which apparently it is possible. – llrs Jun 21 '18 at 18:45