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[go-friends] Reactome Announcement: Edges/ connections between pathways

Balaji balajior at yahoo.com
Tue May 20 05:21:51 PDT 2014


Dear Robin,
Thank you for your reply.
Do you know the Mysql command to extract the same hierarchy for Human as seen in the link below  http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/RESTfulWS/pathwayHierarchy/homo+sapiens

Thank you,
Balaji


On Friday, 16 May 2014 7:06 AM, Robin Haw <Robin.Haw at oicr.on.ca> wrote:
 


Dear Balaji,
You might want to try our restful services to help answer your questions -  http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html. 
Regards,
Robin

From: Balaji <balajior at yahoo.com>
Reply-To: Balaji <balajior at yahoo.com>
Date: Thursday, May 15, 2014 at 11:36 AM
To: "reactome-announce at reactome.org" <reactome-announce at reactome.org>
Subject: Edges/ connections between pathways





Hi,

I would like to extract all the pathways in an organism. In each pathway I want all the genes involved and further identify total number of connections between the pathways.
I know how to extract all the pathways and genes associated with it using Mysql or biomaRt in R.
I am unable to figure out the latter part which is to identify pathway connections 
for eg. in KEGG as example http://www.genome.jp/kegg-bin/show_pathway?hsa00010
Glycolysis : TCA cycle : 1,1
In KEGG there is one outward and one inward connection, i would like to identify such connections between reactome pathways.
Thank you,
Balaji
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