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[bioontology-support] Request/Query

Eamonn Maguire maguire at ebi.ac.uk
Thu Jul 9 11:51:38 PDT 2009


Yeah, sounds good :o)

Eamonn

On 9 Jul 2009, at 19:49, Trish Whetzel wrote:

> Hey Eamonn,
>
> Just getting settled back. Are you available to discuss via Skype?
>
> Trish
>
> From: bioontology-support-bounces at lists.stanford.edu [mailto:bioontology-support-bounces at lists.stanford.edu 
> ] On Behalf Of Eamonn Maguire
> Sent: Thursday, July 09, 2009 11:48 AM
> To: support at bioontology.org
> Subject: [bioontology-support] Request/Query
>
> Hi all,
>
> I sent an email to Trish, but she still hasn't replied yet (i think  
> she is on holiday anyway??) and I'm in a bit of a rush in terms of  
> getting something implemented for the use case i have identified  
> below. i'd be very grateful if you could help with this matter!
>
> We want to be able to not only specify recommended ontologies via  
> the configuration tool, but also where in the ontology tree the  
> terms should come from. For example in EFO you would have the  
> following path in the ontology:
>
> - experimental factor
>           - information entity
>                       - protocol
>                                   | clinical treatment
>                                   | extraction protocol
>                                   + study design
>
> (where - denotes an expanded tree and + denotes a branch which is  
> not expanded :o) )
>
> how could i go about performing a query say on EFO, but only on  
> terms appearing in the 'protocol' branch within BioPortal.
>
> The thing is, i know i can do this programmatically by getting all  
> the terms under protocol branch and then filtering the data out  
> through a simple algorithm, but i wanted to ask you if there was a  
> mechanism which i've missed which could be used to perform such a  
> query just on your side?!
>
> many thanks,
>
> Eamonn Maguire
>
> +          EMBL Outstation - Hinxton,
>               European Bioinformatics Institute,
>               Wellcome Trust Genome Campus,
>               Hinxton,
>               Cambridge, CB10 1SD,
>               United Kingdom
> (          01223 492682
> *          maguire at ebi.ac.uk
> :           http://www.ebi.ac.uk/~maguire
> :     http://www.ebi.ac.uk/net-project
>

--
* 	maguire at ebi.ac.uk
: 	http://www.ebi.ac.uk/~maguire
:     http://www.ebi.ac.uk/net-project










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