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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Allergy Annotator
Date Fri, 10 Jul 2015 19:12:12 GMT
Hi Dima, Tom,

I was thinking the same as Dima's first solution.  Iterate through the medication events and
see any is included in a phrase as mentioned in Tom's original email.  Each phrase structure
would have to be specified beforehand.  However, assigning appropriate CUIs would require
having a lookup table for each medication allergy.  I think that would be the simplest solution.

Sean

-----Original Message-----
From: Dligach, Dmitriy [mailto:Dmitriy.Dligach@childrens.harvard.edu] 
Sent: Friday, July 10, 2015 2:50 PM
To: cTAKES Developer list
Subject: Re: Allergy Annotator

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).


Dima

--
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>>
wrote:

Sean,

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?

Thanks,
Tom

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?

Sean

-----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

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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