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From Tomasz Oliwa <ol...@uchicago.edu>
Subject RE: cTAKES false positives, case-insensitivity
Date Wed, 01 Jun 2016 16:07:26 GMT
Thank you all for the suggestions. 

Sean, by "make the AE case-sensitive" do you mean writing an annotator that simply removes
an annotation based on some criteria like case and semantic type? Or does cTAKES have such
a switch already available?

From: Finan, Sean [Sean.Finan@childrens.harvard.edu]
Sent: Wednesday, June 01, 2016 10:56 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES false positives, case-insensitivity

Oh - I should mention:
Increasing the minimum required span cause have unwanted false negatives.  A minimum of 5
will get rid of things like "arm" and "foot".  You could make your own AE that changes this
by getting rid of only disease/disorder with character count < 5 .  That would probably
be better.  Also maybe meds with count < 5.  You can even make the AE case-sensitive in
case that helps.


-----Original Message-----
From: Tomasz Oliwa [mailto:oliwa@uchicago.edu]
Sent: Wednesday, June 01, 2016 11:28 AM
To: dev@ctakes.apache.org
Subject: cTAKES false positives, case-insensitivity


I have encountered false positives annotated with cTAKES that seem to come from case-insensitivity
of the annotation lookup, such as:

Pt uses hearing aids. -> "aids" is found as DiseaseDisorderMention cui=C0001175, Acquired
Immunodeficiency Syndrome

Pt values are all stable. -> "all" is found as DiseaseDisorderMention cui=C1961102, Precursor
Cell Lymphoblastic Leukemia Lymphoma"

Are there ways in cTAKES to approach or to resolve such issues?

How do you deal with such false positives, so that they are not matched?


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