Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] annotated sentence in the result

Madani,Sina AHMadani at
Thu Jan 26 12:10:29 PST 2012

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 


-----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


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 

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
 > _______________________________________________
 > bioontology-support mailing list
 > bioontology-support at

More information about the bioontology-support mailing list