text: user48: 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.
  
  user1527: 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).
  
  
  user48: 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.
  
original_text: 48: <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>
   1527: <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>
   48: <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>
  