[Bioperl-l] Question about handling ontology files

[Sean Davis]

On 8/9/05 7:05 AM, "Davis, Sean (NIH/NHGRI)" <sdavis2 at mail.nih.gov> wrote:

> 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.

I forgot to mention the EASIEST way to do this.  If you have SOURCE output,
you can include locuslink IDs that you can use to put into various online or
standalone ontology analysis packages.  See this link for a recent review:

http://bioinformatics.oxfordjournals.org/cgi/reprint/bti565v1