Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

How to get the relationships between all pairs of GO terms in the GO hierarchy

Mike Cherry cherry at genome.Stanford.EDU
Mon Feb 16 21:00:43 PST 2004


One possibility is to use the goPath scripts from SGD.  You'll find it 
at the GO FTP site at:

The README has details about the output.  You'll want to use the file on the three ontology go/ontology/ directory. reads the ontology file and outputs a TAB-delimited 
file that explicitly states all the paths between nodes.  On my home 
Mac the script runs in a few seconds for each ontology file.


On Feb 16, 2004, at 5:42 PM, Sarath Chandra Janga wrote:

> Dear all
>    Could someone tell which is the best way to get the relationships
> between any pair of GO terms in the GO hierarchy(whether they have a
> parent-child relationship or not) into a simple flat file
> format.
>  Any help would be appreciated
> regards
> sarath

This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at
Subscribing   send   "subscribe"   to   gofriends-request at
Unsubscribing send   "unsubscribe"  to  gofriends-request at

More information about the go-friends mailing list