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[Gofriends] matrices from terms

Nicholas Mitsakakis n.mitsakakis at utoronto.ca
Fri Nov 14 10:40:14 PST 2008


Hello GO friends,

I have a list of N GO terms and I would like to generate two N by N 
binary matrices. In the first (let's call it parent-child) matrix the 
entry (i,j) will be 1 if and only if the i-th GO term is a parent of the 
j-th term. At the second (ancestors-descendants) matrix 1's at (i,j) 
entry will mean that i term is an ancestor of j term.

I am interested only in the BP ontology and also, only in "is_a" 
relationships.

If you could point out some tools that could do that, I would appreciate 
it. I would prefer to use an older .obo file I have, so I would like the 
tool to accept the obo file as input.

I probably need to do this only once (and I only have few terms) so 
on-line tools should be fine.

Thanks,

Nicholas

-- 
Nicholas Mitsakakis
PhD Candidate - Biostatistics
Dalla Lana School of Public Health Sciences
University of Toronto, Canada




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