Answers.Body: <p>If you like to get pathways and corresponding genes as simple table format in a plain text file, use <a href="https://www.biostars.org/p/108669/" rel="nofollow noreferrer">GeneSCF</a> 'prepare_database' module. This can be simple solution.</p>
  
  <p><strong>FTP vs API</strong>:</p>
  
  <p>The differences I see is,</p>
  
  <ul>
  <li><p>quick access to the updated content via FTP. With that I assume using <a href="https://www.bioinformatics.jp/en/keggftp.html" rel="nofollow noreferrer">FTP version</a> you will have access to weekly database updates. Also bulk download is possible and more convenient via FTP subscription. </p></li>
  <li><p>But <a href="https://www.kegg.jp/kegg/rest/" rel="nofollow noreferrer">KEGG REST API</a> updates once in month or two months or a year (not a recently updated contents).</p></li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-14T14:32:46.360Z
Answers.Text: 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?
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-14T14:38:26.983Z
Answers.Text: 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.
Answers.UserDisplayName: EagleEye
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-14T14:43:54.240Z
Answers.Text: I've read the relevant parts of it and it didn't answer my question.
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-14T14:47:58.413Z
Answers.Text: 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.
Answers.UserDisplayName: EagleEye
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-14T14:55:36.843Z
Answers.Text: Oh, that got already answered in the other answer. Thanks, and my apologies
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-14T15:06:36.040Z
Answers.Text: 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?
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-14T15:15:38.913Z
Answers.Text: 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.
Answers.UserDisplayName: EagleEye
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-14T15:29:29.817Z
Answers.Text: 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).
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-14T14:01:37.717Z
Answers.LastActivityDate: 2018-06-14T15:38:16.390Z
Answers.LastEditDate: 2018-06-14T15:38:16.390Z
Answers.UserDisplayName: EagleEye
Answers.Body: <p>We implemented <a href="https://github.com/bio2bel/kegg" rel="nofollow noreferrer">Bio2BEL KEGG</a> package to download the KEGG database via its RESTful API</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-21T18:45:40.367Z
Answers.Text: 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.
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-21T18:35:11.780Z
Answers.LastActivityDate: 2018-06-21T18:44:44.060Z
Answers.LastEditDate: 2018-06-21T18:44:44.060Z
Answers.UserDisplayName: ddomingo
Answers.Body: <p>I found the way to download the <a href="http://rest.kegg.jp/link/pathway/hsa" rel="nofollow noreferrer">genes and pathways</a> thanks to this answer using <a href="https://support.bioconductor.org/p/109871/#109959" rel="nofollow noreferrer">KEGGREST</a>. </p>
  
  <p>It seems that the <a href="https://www.kegg.jp/kegg/rest/keggapi.html" rel="nofollow noreferrer">API</a> allows to fully download the database because it allows to download info, list, find, get, conv, link, ddi.</p>
  
  <p>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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-13T08:25:47.883Z
Answers.LastActivityDate: 2018-06-13T08:25:47.883Z
Answers.UserDisplayName: llrs
Body: <p>I was reading the KEGG <a href="https://www.kegg.jp/kegg/docs/plea.html" rel="noreferrer">plea</a> and I found that it doesn't forbid using the KEGG API. Then, what is in the FTP server <a href="https://www.bioinformatics.jp/docs/subscription_personal.pdf" rel="noreferrer">license for personal use/academic use</a> that it is not covered by the API?</p>
  
  <p>Or I could download all the database via the API?</p>
  
  <p>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.</p>
  
Tags: <database><kegg>
Title: KEGG FTP vs KEGG API
ThreadText: # KEGG FTP vs KEGG API
  
  (Asked by: username_0 on 2018-06-01)
  
  I was reading the KEGG [plea](https://www.kegg.jp/kegg/docs/plea.html) 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](https://www.bioinformatics.jp/docs/subscription_personal.pdf) 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.
  
  **Tags:** database, kegg
  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_0 on 2018-06-13. Score: 2 | Accepted answer
  
  I found the way to download the [genes and pathways](http://rest.kegg.jp/link/pathway/hsa) thanks to this answer using [KEGGREST](https://support.bioconductor.org/p/109871/#109959).
  
  It seems that the [API](https://www.kegg.jp/kegg/rest/keggapi.html) 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.
  
  
  ---
  
  ### Answer by username_1 on 2018-06-14. Score: 1
  
  If you like to get pathways and corresponding genes as simple table format in a plain text file, use [GeneSCF](https://www.biostars.org/p/108669/) '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](https://www.bioinformatics.jp/en/keggftp.html) you will have access to weekly database updates. Also bulk download is possible and more convenient via FTP subscription.
  * But [KEGG REST API](https://www.kegg.jp/kegg/rest/) updates once in month or two months or a year (not a recently updated contents).
  
  > **Comments:**
  > **username_0**: 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?  
  > **username_1**: 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.  
  > **username_0**: I've read the relevant parts of it and it didn't answer my question.  
  > **username_1**: 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.  
  > **username_0**: Oh, that got already answered in the other answer. Thanks, and my apologies  
  > **username_0**: 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?  
  > **username_1**: 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.  
  > **username_0**: 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).  
  
  ---
  
  ### Answer by username_2 on 2018-06-21. Score: -1
  
  We implemented [Bio2BEL KEGG](https://github.com/bio2bel/kegg) package to download the KEGG database via its RESTful API
  
  > **Comments:**
  > **username_0**: 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.  
  
  ---
  
  