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[go-helpdesk] Software GO Help query

Seth Carbon sjcarbon at lbl.gov
Tue Jun 26 15:27:10 PDT 2012


Vishal,

Taking a look at your query and assuming that I'm understanding you
correctly, you seem to be searching for a term with a name something
like "pax4". However, what I think you want to be looking for in this
case is a gene product symbol like "pax4"--the query might look like:

SELECT DISTINCT
 gene_product.symbol,
 term.name,
 term.acc
FROM
 gene_product,
 term,
 association,
 species
WHERE
 gene_product.species_id = species.id AND
 species.ncbi_taxa_id = 9606 AND
 gene_product.symbol LIKE '%pax4%' AND
 association.term_id = term.id AND
 association.gene_product_id = gene_product.id AND
 association.is_not = 0

Best wishes,

-Seth


On 06/26/2012 05:08 AM, Paola Roncaglia wrote:
> Dear Vishal,
> 
> Thank you for contacting GO.
> I am forwarding your message to the GO Software group so they may help
> with your query. They are on the West Coast, so it may be a few hours
> before they get back to you.
> 
> Please feel free to contact us again if you have any more queries.
> With best regards,
> 
> Paola Roncaglia, for GO help.
> 
> 
>> Subject:
>> GO Help query (from website)
>> From:
>> vishal at mit.edu
>> Date:
>> Fri, 22 Jun 2012 11:14:49 -0700
>>
>> To:
>> go-helpdesk at mailman.stanford.edu
>>
>>
>> Email: vishal at mit.edu
>> Name: Software (from vishal saxena)
>> Text: Hi,
>> Could you please suggest what query I should input if I want to replicate amigo results for gene or protein names? For example, I have the following query but it seems not to give me amigo-like results:
>> ------------------------------query in perl----------
>> 	$query = "select DISTINCT gene_product.symbol FROM gene_product, term, association, species WHERE 
>> 	 gene_product.species_id = species.id AND
>> 	 species.genus = 'Homo' AND species.species = 'sapiens' AND 
>> 	 upper(term.name) LIKE '%".uc($line)."%' AND
>> 	 association.term_id = term.id AND 
>>  	 association.gene_product_id = gene_product.id AND
>> 	 association.is_not = 0";
>> ----------------end query------------------
>> for example, I get no hits when I try pax4 with the above query, but in amigo I get 10 and 5 hits for home sapiens.
>>
>> Thanks very much. I appreciate any help you can provide. I am essentially trying to obtain groups of genes listed by symbol automatically.
>>
> 
> -- 
> Dr Paola Roncaglia
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD 
> p: +44 1223 492600
> f: +44 1223 494468 
> 
> 
> 
> _______________________________________________
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> go-helpdesk at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/go-helpdesk



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