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[bioontology-support] Request/Query

Eamonn Maguire maguire at
Thu Jul 9 11:48:07 PDT 2009

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,
	Cambridge, CB10 1SD,
	United Kingdom
( 	01223 492682
* 	maguire at

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