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[bioontology-support] Context Value in Annotator Service

Clement Jonquet jonquet at lirmm.fr
Fri Apr 13 05:32:47 PDT 2012


Hi Vivek, 

 

Be sure to have the parameter withContext=true, otherwise you will not see
the <context> element in the returned  XML.

 

FYI: the withContext parameter is here if you explicitly wants to know why
each annotation (direct or not) was created. For instance, annotating the
text “skin melanoma and melanoma are bad cancer” with only ontology 46453
will return:

-          2 annotations with term 46453/DOID:1909 but with different
contexts if withContext=true

-          1 annotation with term 46453/DOID:1909 but without context if
withContext=false.

 

In that second case what you want to look at is the score of the annotation
that represents the fact that in your text “melanoma” was more present than
“cancer”.

Try it out at: http://rest.bioontology.org/test_oba.html 

 

I hope it helps ;)

Clement

 

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Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor

 

 <mailto:jonquet at lirmm.fr> jonquet at lirmm.fr

 <http://www.lirmm.fr/~jonquet> http://www.lirmm.fr/~jonquet 

 

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                LIRMM

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                34095 Montpellier Cdx 5

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De : bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] De la part de Trish
Whetzel
Envoyé : vendredi 13 avril 2012 11:08
À : Vivek Juluri
Cc : support at bioontology.org
Objet : Re: [bioontology-support] Context Value in Annotator Service

 

Hi Vivek, 

 

The context or characters matched from the input text can be found by using
the <from> and <to> attributes within the annotationBean under <context>.

 

Trish  

 

 



 

 

 

On Apr 10, 2012, at 10:37 AM, Vivek Juluri wrote:








Hi,

 

In my current application i am using Annotator Service. I am using rest
service http://rest.bioontology.org/obs/annotator and i am getting XML
properly. but in that XML i am unable to find Context value.

 

In the Biportal site http://bioportal.bioontology.org/annotator it is
showing the Context in the result grid. How should i get the Context value
from XML?

 

Please let me know if need any more information from my side.

 

-- 

Thanks,

Vivek


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