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[Gofriends] matrices from terms

Chris Mungall cjm at berkeleybop.org
Fri Nov 14 11:06:35 PST 2008


The generally recommended way to do this is via the graph_path table  
in the GO database. You can query either a local installation, or a  
public mirror, via
http://berkeleyop.org/goose. The documentation for this table is here:
	http://www.geneontology.org/GO.database.schema.shtml#go-optimisations.table.graph-path

However, at this time this table contains the transitive closure  
computed by considering all edges, ignoring edge labels (relations).  
Thus it does not satisfy your requirement that only the is_a relation  
is considered

Within the next few months the graph_path table will include the  
relationship type too. See the above docs.

Unfortunately, if you want to use arbitrary .obo files then you would  
have to load your own database instance - this may not be practical  
for you.

Given these two requirements, your best bet may be to download and  
install OBO-Edit2 (currently beta status). This will give you a  
command line script called "obo2linkfile". Run this on any obo file,  
it will generate a table of all inferred child-relation-parent edges.  
You can extract the is_a links and BP nodes from this fairly easily.  
It runs in a few seconds on the current GO. The equivalent script is  
not part of OBO-Edit1.

Unfortunately, this doesn't fit your online requirement - it requires  
a download + install

There are other ways to achieve the same thing of course. I can  
provide more details on the methods above if they fit your requirements.


On Nov 14, 2008, at 6:40 PM, Nicholas Mitsakakis wrote:

> 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
>
> _______________________________________________
> Gofriends mailing list
> Gofriends at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/gofriends
>




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