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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


Sarath,

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

	ftp://ftp.geneontology.org/go/software/SGD/goPath/

The README has details about the output.  You'll want to use the 
parseOntology.pl file on the three ontology go/ontology/ directory.  
parseOntology.pl 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.

-Mike



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
>
>


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