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[go-helpdesk] nuclear functions

Susan Tweedie sart2 at gen.cam.ac.uk
Thu Jun 21 06:57:11 PDT 2012


Dear Richard

Thank you for contacting the GO Consortium with your question.

Unfortunately there isn't an easy way to do this as this information  
is not systematically recorded in the ontology.

The only suggestions our ontology editors could come up with was to do  
a search for any terms (and its decendants) that have 'DNA' or  
'nucle*' in their name. Obviously this type of search won't   
necessarily give you functions or processes that  happen in the  
nucleus (e.g. 'response to DNA damage' may involve proteins in other  
part of the cell, 'viral genome packaging' isn't nuclear. 'DNA  
binding' could be mitochondrial) but it may help you narrow the options.

It may also be worth searching for any term that has an occurs_in  
relations in its cross-products to nucleus or one of its children.  
However we started using the occurs_in relationship for new cross- 
products quite recently so there are unlikely to be many nuclear terms  
defined this way. (Note these are only found in the xp version of the  
ontology).

Sorry we can't be of more help.

Best wishes,

Susan Tweedie

On 20 Jun 2012, at 20/Jun/2012 11:37:29, go-helpdesk-bounces at lists.stanford.edu 
  wrote:

>
> From: rfrancis at ichr.uwa.edu.au
> Date: 20 June 2012 10:45:32 BST
> To: go-helpdesk at mailman.stanford.edu
> Subject: GO Help query (from website)
>
>
>
> Email: rfrancis at ichr.uwa.edu.au
> Name: General query (from Richard Francis)
> Text: Dear Helpdesk,
>
> I have some protein domain data from InterproScan that has  
> associated GO terms for about 350 proteins. What I would like to do  
> is establish a list of those domains and consequently proteins that  
> are associated with a nuclear function (eg DNA binding etc). Now if  
> I have Cellular Component annotation of Nucleus or a child term  
> thereof then that's easy but is there a way of establishing  
> Molecular Function or Biological Process terms that are associated  
> with nuclear activity specifically. Ideally I'd like to be able to  
> do this using the Perl API but if a static list can be generated  
> somehow then I can happily work with this.
>
> Many thanks for any help you can give.
>
> Kind regards,
>
> Richard
>
>

Susan Tweedie
FlyBase GO curator

s.tweedie at gen.cam.ac.uk



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