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[go-helpdesk] GO:0032502 data

Susan Tweedie sart2 at gen.cam.ac.uk
Wed Jun 20 03:36:04 PDT 2012


Dear Bilian

Thank you for contacting the GO Consortium with your question.

Usually you would be able to view all of the gene products  
associations for a GO term by searching AmiGO (http://amigo.geneontology.org 
) with that term and then clicking the gene product associations (top  
right). You then get the option to  'Download all association  
information in: gene association format or RDF-XML'.

However as you may have already discovered, this isn't possible for GO: 
0032502 (developmental process) because the number of associations  
with this term exceeds the capacity of our current software.

I would generally suggest that you use the filter options to restrict  
the data set to specific species or consider excluding some types of  
evidence but since developmental process is such a high level term  
even filtering will result in too many associations for many species.

Assuming you don't want to select a more specific child term for your  
search, I think that you are probably best to use QuickGO instead.

http://www.ebi.ac.uk/QuickGO/

Search with your term then select protein annotation which gives a  
download option (top right). Note that QuickGO contains electronic  
annotations (IEA evidence) for many more species than AmiGO does and  
consequently the number of associations with GO:0032502 is  
substantially higher than AmiGO - you may want to considering  
filtering the data set by species or evidence before downloading it.  
However it is possible to download the entire data set by raising the  
default value from 1000 to 500,000 in the download box. There is also  
the option to zip the file.

If this does not answer your question then please get back to us.

Best wishes,
Susan Tweedie


On 19 Jun 2012, at 19/Jun/2012 12:04:35, go-helpdesk-bounces at lists.stanford.edu 
  wrote:

>
> From: bjin at georgiahealth.edu
> Date: 18 June 2012 19:06:23 BST
> To: go-helpdesk at mailman.stanford.edu
> Subject: GO Help query (from website)
>
>
>
> Email: bjin at georgiahealth.edu
> Name: Ontology (from bilian jin)
> Text: I want to view the data   of  GO:0032502. Can you tell me how  
> to download this data?
>
>

Susan Tweedie
FlyBase GO curator

s.tweedie at gen.cam.ac.uk



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