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

Chris Mungall cjm at fruitfly.org
Mon Apr 16 14:41:59 EDT 2007


Unless the Entrez interface has changed since I last looked, the  
query below for "pyrimidine ribonucleotide biosynthetic process" will  
NOT perform the transitive closure over the graph; this means genes  
and gene products annotated to GO:0009174 "pyrimidine ribonucleoside  
monophosphate biosynthetic process", for example

On Apr 16, 2007, at 9:25 AM, Chris Fields wrote:

> 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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