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

Chris Fields cjfields at uiuc.edu
Mon Apr 16 15:25:14 EDT 2007


You are correct; it explains why the list is only 120 genes.  The  
only way (currently) to do so would be to perform the closure locally  
somehow (maybe via go-perl or similar).

chris

On Apr 16, 2007, at 1:41 PM, Chris Mungall wrote:

>
> 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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>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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