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

Chris Fields cjfields at uiuc.edu
Mon Apr 16 12:25:42 EDT 2007


You can limit EntrezGene searches by Gene Ontology ID using the [Gene  
Ontology] field in queries.  The following query:

'9220[Gene Ontology]'

will give 120 gene IDs.  You can get the same list using the still- 
under-development Bio::DB::EUtilities (usual EUtilities caveat: I'm  
still working on this):

my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                        -db => 'gene',
                                        -term => '9220[Gene Ontology]',
                                        -retmax => 300);
$esearch->get_response;
my @ids = $esearch->get_ids;
print join "\n", at ids;

In my opinion, Sean's idea of using SQL is probably better if you  
have tons of searches to do.

chris

On Apr 16, 2007, at 9:36 AM, Wijaya Edward 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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