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[bioontology-support] Request/Query

Trish Whetzel whetzel at
Thu Jul 9 11:49:14 PDT 2009

Hey Eamonn, 


Just getting settled back. Are you available to discuss via Skype?




From: bioontology-support-bounces at
[mailto:bioontology-support-bounces at] On Behalf Of Eamonn
Sent: Thursday, July 09, 2009 11:48 AM
To: support at
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


- 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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