[Bioperl-l] Question about handling ontology files

[Sean Davis]

On 8/8/05 10:01 PM, "iluminati at earthlink.net" <iluminati at earthlink.net>
wrote:

> Here's my situation.  I have a bunch of ontologies downloaded from a
> batch run on SOURCE.  What I want to be able to do is parse these files
> so I can count the different numbers of instances of terms within all 3
> sets of ontological descriptions (biological process, cellular component
> and molecular function).  Is there something in Perl or another program
> that could help me out with this situation?  Any information that you
> have would be useful to me.  Thanks

I think you will have to parse the SOURCE files yourself.  After that is
done, there are several options including go-perl (from
http://www.geneontology.org), Bioperl (Bio::OntologyIO and relatives), and
GO-TermFinder (on CPAN).  I'm not sure which is going to be the best option
for you.  

If you are comfortable with RDBMs, you could download the tables from the GO
mysql database and do lookups yourself using DBI.

Hope this helps,
Sean