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[bioontology-support] NCBO Annotator Service parameter isVirtualOntologyId not working as expected.

Clement Jonquet jonquet at
Tue Jul 16 22:35:45 PDT 2013

Hi Zach, 


>From what I see with :

localOntologyId 47282 is not parsed for the Annotator yet (or anymore).

So this is normal you don’t get any hit.


The version of Gazetteer that is here is : 50311 or 1397

If you use the “isVirtualOntologyId=true” parameter be sure to use
virtualOntologyId it for all the parameters (and respectively
localOntologyId otherwise). But it seems his is what you’re doing.


Please, note also that the ontologiesToExpand parameter is only useful if
you use the mapping semantic expansion
 the role of this parameter is to
explicit the ontologies to use for mapping semantic expansion then the
parameter ontologiesToKeepInResult explicit the list of ontologies in which
you want your results back.


Only Ray at NCBO can tell you if 47282 can be put back in the Annotator back


Hope it helps.




De : bioontology-support-bounces at
[mailto:bioontology-support-bounces at] De la part de Zach
Envoyé : mercredi 17 juillet 2013 06:22
À : support at; Patrice Seyed
Objet : [bioontology-support] NCBO Annotator Service parameter
isVirtualOntologyId not working as expected.




I am trying to make a query to a specific version of the Gazetteer Ontology
(47282) using the Annotator Service REST API. 

I have set the parameter 'isVirtualOntologyId' to 'false', and then set
parameters 'ontologiesToExpand' and 'ontologiesToKeepInResults' to '47282',
and am expecting to get results.


Now, when I try to annotate the text 'Crystal Lake' with the above
parameters, I get no returned results, and a blank response from a query to
the service. 


When I set the 'ontologiesToExpand' and 'ontologiesToKeepInResults' to the
version of the Gazetteer Ontology that is pointed to by its virtual id
(50311), and try to annotate the text 'Crystal Lake', I get a concept
definition for an instance of Crystal Lake. 

Likewise, when I set 'isVirtualOntologyId' to 'true', and set
'ontologiesToExpand' and ontologiesToKeepInResults' to '1397'(the virtual ID
for GAZ), then I get the same concept definition for 'Crystal Lake' as
above, which is to be expected.


I want to load concepts from the version 47282, and my diagnosis is that the
Annotator Service is not returning concepts for this version. 


Is there a quick fix for this? I am in the middle of writing a paper that
has a deadline relatively soon.


Zach Fry


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