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Re: [HCLSIG] homologs for yeast proteins?

From: Brian Osborne <osborne1@optonline.net>
Date: Tue, 31 Jan 2006 15:03:48 -0500
To: jluciano@predmed.com, public-semweb-lifesci@w3.org
Cc: jluciano@gmail.com
Message-id: <C0052CD4.711B%osborne1@optonline.net>

Joanne,

If you're interested in doing this query manually you can use Entrez Gene (
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene), something
like:

mitochondrial [go] AND signaling [go] AND pathway [go]

What I _don't_ know is whether you're querying with any child terms as well,
presumably you want to find genes with the children assigned to them.

As you know Entrez Gene assigns ontology terms to genes, and all of their
proteins inherit the term, functionally speaking.

You could also do this using Bioperl, if your colleague would like to write
a script.

Brian O.


On 1/31/06 2:27 PM, "Joanne Luciano" <jluciano@predmed.com> wrote:

> 
> Hi,
> 
> An MD I met with last week mentioned briefly the desire to obtain homologs
> for yeast proteins with the GO ID 0031930.  With it was a request for other
> suggestions for querying proteins with this ontology assignment (looking for
> mammalian homologs).
> 
> Can the semantic web help with this or is it already basic and solved, in
> which case, can someone point me or fill in the details?  Where should I go?
> What questions should I  ask?
> 
> Joanne
> 
> 
> 
Received on Tuesday, 31 January 2006 20:04:21 GMT

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