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[Gofriends] matrices from terms

Mary Dolan Mary_Dolan at
Fri Nov 14 11:34:50 PST 2008

Nicholas Mitsakakis <n.mitsakakis at> writes:
>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" 

Hi, Nicholas.
I have a simple perl script that parses a gene_ontology.obo file and generates a (tab-delimited text) list of term-ancestor pairs. I'm happy to send that to you if it would be useful.

Mary E. Dolan, Ph.D.
Mouse Genome Informatics Consortium, The Jackson Laboratory
mdolan at

Research Faculty, NCGIA
Department of Spatial Information Science and Engineering, University of Maine
Boardman Hall 329
University of Maine
Orono, Maine 04469
fax: 207.581.2206
mary_dolan at

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