[Bioperl-l] Extracting Gene Names Genome Ontology (GO) with Perl

Chris Mungall cjm at fruitfly.org
Mon Apr 16 14:49:23 EDT 2007


Download:
http://search.cpan.org/~cmungall/go-db-perl

or do:

cpan GO::AppHandle

The API call you want is here:
http://search.cpan.org/~cmungall/go-db-perl/GO/ 
AppHandle.pm#get_deep_products

Here is an example snippet:

   use GO::AppHandle;
   my $apph=GO::AppHandle->connect(@ARGV);
   my $go_acc = shift @ARGV;
   my $gps = $apph->get_deep_products({term=>{acc=>$go_acc}});
   foreach my $gp (@$gps) {
     printf "%s %s\n", $gp->xref->acc, $gp->symbol;
   }

You will need to download the GO Database.

Cheers
Chris

On Apr 16, 2007, at 8:14 AM, Wijaya Edward wrote:

>
> Hi Spiros,
>
> Thanks for your reply. I am interested to apply it for
> all the kind of organisms related to that particular GO ID.
>
> Do you have a CPAN module for that?
> --
> Edward WIJAYA
> SINGAPORE
>
> ________________________________
>
> From: s.denaxas at gmail.com on behalf of Spiros Denaxas
> Sent: Mon 4/16/2007 11:10 PM
> To: Wijaya Edward
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Extracting Gene Names Genome Ontology (GO)  
> with Perl
>
>
>
> Hi Edward,
>
> What organism are you interested in? I have some code from my PhD
> based on the Saccharomyces cerevisiae genome. Basically uses the SGD
> flat files and a local MySQL instance of GO. Might be worth turning
> into modules if people are interested in it, although it is pretty
> organism oriented and the lack of abstraction might introduce a number
> of problems.
>
> Spiros
>
> On 4/16/07, Wijaya Edward <ewijaya at i2r.a-star.edu.sg> wrote:
>>
>> Dear all,
>>
>> Given a GO id, is there a way to extract all
>> the related gene names from that id with Perl?
>>
>> Anybody has experience with that?
>> I've looked through GO module in CPAN, but can't seem
>> to find any tool that facilitated that searc
>>
>> Look forward very much for your advice.
>>
>> --
>> Edward WIJAYA
>> SINGAPORE
>>
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