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From "Dligach, Dmitriy" <Dmitriy.Dlig...@childrens.harvard.edu>
Subject Re: Allergy Annotator
Date Fri, 10 Jul 2015 18:49:51 GMT
Hi Tom,

If the patters are pretty simple, you could just add a few rules on top of the cTAKES dictionary
lookup output. Something of the kind “allergic to <medication>” or “allergies:
<medication1>, <medication2>, <substance1>, ...”.

If these patterns are hard to express as rules, you should consider a machine learning based
sequence labeling route (e.g. something similar to the cTAKES chunker).


Dmitriy (Dima) Dligach, Ph.D.
Boston Children's Hospital and Harvard Medical School
(617) 651-0397

On Jul 10, 2015, at 13:40, Tom Devel <develxy@gmail.com<mailto:develxy@gmail.com>>


It would be a wider net, such that if an allergy is mentioned in the
clinical note, this is captured in the corresponding IdentifiedAnnotation
(or alternatively, if the IdentifiedAnnotation class should not be changed
with a new attribute, in a separate allergy annotation).

This annotator would then have to of course run after the clinical pipeline
has run and discovered all IdentifiedAnnotations.

I am familiar with writing UIMA/cTAKES annotators, but not sure how a new
ML method could be integrated here for detecting allergies. Do you have any
thoughts about how to approach this in general?


On Fri, Jul 10, 2015 at 11:54 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.harvard.edu>> wrote:

Hi Tom,

Are you interested in catching all allergies or just a few specific
allergies for a study?  If you are only concerned with a few then there is
a (possibly) simple solution.  If you are interested in throwing a wider
net then I think that a new module would need to be created; does anybody
reading this have an ML or regex style module?


-----Original Message-----
From: Tom Devel [mailto:develxy@gmail.com]
Sent: Friday, July 10, 2015 12:42 PM
To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
Subject: Allergy Annotator


I would like to use/extend cTAKES to detect allergies.

In the cTAKES publication (2010)

there is the mention
that: "Allergies to a given medication are handled by setting the negation
attribute of that medication to ‘is negated’."

However, in a post here in 2014 (RE: Allergy Indication) it is said that
cTAKES does not have a module for allergy discovery.

1. What is the current status of allergy detection in cTAKES?

2. I did some testing, while cTAKES discovers concepts about allegies
("wheat allergy" is found as C0949570), using "ALLERGIES:  PENICILLIN,
WHEAT" or "The patient is allergic to penicillin." does not give penicillin
or wheat annotations allergy status.

How would I go about detecting these allergy mentions?


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