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[bioontology-support] annotated sentence in the result

Paul R Alexander palexander at
Thu Jan 26 13:09:18 PST 2012

There is a parameter you can use to restrict results to only show the 
longest phrase matched (longestOnly=true). However, there is a known bug 
that causes bad results if you also filter on a subset of ontologies, so 
only use it when you are annotating with all ontologies in the system.

If you used the parameter with your results below, then "family history 
of heart failure" would match, but "heart" and "heart failure" would not.

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research

On 1/26/12 12:10 PM, Madani,Sina wrote:
> So, if I have "heart failure" in multiple phrases/sentences in a paragraph (that is passed as the text to annotate) I can't differentiate the returned mapping from the phrase "past family medical history of heart failure" or the phrase "heart surgery due to heart failure" unless I count the words.
> We often need to look at the context to verify the correct mapping. So in the case above, a code associated with a "family history of heart failure" would be the correct one versus a code for "history of heart failure"
> Thank you Paul for clarification
> Sina
> -----Original Message-----
> From: Paul R Alexander [mailto:palexander at]
> Sent: Thursday, January 26, 2012 1:59 PM
> To: Madani,Sina
> Cc: support at
> Subject: Re: [bioontology-support] annotated sentence in the result
> Sina,
> When looking at the XML formatted results, in each annotation returned
> there are two concepts: one at /annotationBean/concept and another under
> /annotationBean/context. In the context, there is are "from" and "to"
> elements that give the character count where the annotation match is
> located in your original text.
> In addition, if you need the original text that you sent to the service,
> this is available in the parameters section under the element titled
> "textToAnnotate".
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> On Thu Jan 26 11:35:25 2012, Madani,Sina wrote:
>   >  Hi,
>   >
>   >  Assuming that I am sending a multi phrase/sentence as the
>   >  text-to-annotate to Bioportal, is there any parameter available to
>   >  include the original phrase/sentence that a mapping concept is found?
>   >
>   >  Thanks!
>   >
>   >  Sina
>   >
>   >
>   >
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