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[go-helpdesk] Software GO Help query

Paola Roncaglia paola at ebi.ac.uk
Tue Jun 26 05:08:12 PDT 2012


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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