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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Allergy Annotator
Date Fri, 10 Jul 2015 16:54:41 GMT
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?

Sean

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

Hi,

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

In the cTAKES publication (2010)
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC2995668_&d=BQIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZApJmGKjzvFfNco5rRFVwSIyxmg4MRsxakfuXHbMZME&s=mGWu0XBCJqG2MI5qPlwIpGbQL5IYe7t5EWcvhPYW7Lo&e=
 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?

Thanks,
Tom
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