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

Wijaya Edward ewijaya at i2r.a-star.edu.sg
Mon Apr 16 23:51:18 EDT 2007


Thanks so much for all the suggestion.
It was really helpful to me. 
 
--
Edward WIJAYA

________________________________

From: Chris Mungall [mailto:cjm at fruitfly.org]
Sent: Tue 4/17/2007 8:59 AM
To: Chris Fields
Cc: bioperl-l at lists.open-bio.org; Wijaya Edward
Subject: Re: [Bioperl-l] Extracting Gene Names Genome Ontology (GO) with Perl




You could perform the closure locally and then iterate over the 
individual IDs or construct a big disjunctive query to Entrez - 
either way it's not so efficient, especially for less specific nodes 
(distributed queries with ontologies is an interesting challenge).

Soon you'll be able to do the same query over the GO Database / AmiGO 
using a REST API

On Apr 16, 2007, at 12:25 PM, Chris Fields wrote:

> 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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