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[Gofriends] matrices from terms

Mary Dolan Mary_Dolan at umit.maine.edu
Fri Nov 14 11:34:50 PST 2008


Nicholas Mitsakakis <n.mitsakakis at utoronto.ca> 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" 
>relationships.

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.
Cheers,
Mary

Mary E. Dolan, Ph.D.
************************************
Mouse Genome Informatics Consortium, The Jackson Laboratory
mdolan at informatics.jax.org
(207)288-6439

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 umit.maine.edu
************************************




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