SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
KEGG vs MetaCyc joscarhuguet General 1 09-19-2012 06:40 PM
pathways API KEGG svl Bioinformatics 5 02-10-2011 02:37 PM

Reply
 
Thread Tools
Old 11-12-2013, 08:45 AM   #1
dietmar13
Senior Member
 
Location: Vienna

Join Date: Mar 2010
Posts: 107
Default sus scrofa (pig) KEGG pathways: where to find...

hello,

does someone know where to download KEGG pathways (xml) for sus scrofa (pig) (or have them to share).

thank you,

dietmar
dietmar13 is offline   Reply With Quote
Old 11-12-2013, 09:01 AM   #2
LeightonP
Member
 
Location: Scotland

Join Date: Feb 2011
Posts: 29
Default

KEGG is a good place to get KEGG pathways

http://www.genome.jp/kegg-bin/show_p...scription=show

is a link for fatty acid biosynthesis in Sus scrofa (pig). You can download the KGML from there, or with the link:

http://www.kegg.jp/kegg-bin/download...61&format=kgml

The other pig pathways all start with ssc; the numbers refer to the pathway.

There's also a REST-style API:

http://www.kegg.jp/kegg/docs/keggapi.html
LeightonP is offline   Reply With Quote
Old 11-12-2013, 09:01 AM   #3
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,550
Default

I think you will need to obtain a subscription to download those.

API restrictions clearly state that it should not be used for bulk downloads.

Last edited by GenoMax; 11-12-2013 at 09:03 AM.
GenoMax is online now   Reply With Quote
Old 11-12-2013, 09:25 AM   #4
dietmar13
Senior Member
 
Location: Vienna

Join Date: Mar 2010
Posts: 107
Default yes, but

@leightonP

I know the KEGG homepage but I didn't find a download page...

@GenoMax

I thought there could be some collections around, downloaded before they got commercial,...
dietmar13 is offline   Reply With Quote
Old 11-13-2013, 11:55 AM   #5
LeightonP
Member
 
Location: Scotland

Join Date: Feb 2011
Posts: 29
Default

Quote:
Originally Posted by dietmar13 View Post
@leightonP

I know the KEGG homepage but I didn't find a download page...
There's a download link on each individual page: "Download KGML" - 4th from the left on the first page I linked to.

If you're abiding by the terms of the KEGG API, then you probably shouldn't bulk download, even though it's easy enough to, using something like this: https://github.com/widdowquinn/KGML
LeightonP is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:38 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO