[Bioperl-l] Extracting Gene Names Genome Ontology (GO) with Perl
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).
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
>> -retmax => 300);
>> 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.
>> 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
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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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Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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