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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Allergy Annotator
Date Fri, 10 Jul 2015 20:20:19 GMT
Hi Tom,

It is exactly because the sentence detector splits "KEY:" from "VALUE" that I didn't suggest
using sentences.  Instead, I would just iterate over the whole cas collection of medication
events and attempt to match allergy phrases  ("allergic to medication") with text the note
spanning from event.begin-15 to event.end+15 or whatever window size you prefer.

Sean

-----Original Message-----
From: Tom Devel [mailto:develxy@gmail.com] 
Sent: Friday, July 10, 2015 4:12 PM
To: dev@ctakes.apache.org
Subject: Re: Allergy Annotator

Sean and Dima, these are great suggestions, thanks so far.

Sean, when looping over medication events as you say, I can see how it is possible to take
the textspan.Sentence of this MedicationMention, and then do a regex check for the phrase
structure as Dima said.

But instead of textspan.Sentence, you mention "see any is included in a phrase". What cTAKES/UIMA
class is related to this?

Because if I would use textspan.Sentence, it would work for "The patient is allergic to penicillin.",
but cTAKES splits "ALLERGIES:  PENICILLIN, WHEAT"
into two sentences, so that the MedicationMentions here would not be in the same sentence
as the word "ALLERGIES".

Thanks again,
Tom


On Fri, Jul 10, 2015 at 2:12 PM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:

> 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.e
> du>>
> 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.g
> ov_pmc_articles_PMC2995668_&d=BQIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZM
> SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZApJmGKjz
> vFfNco5rRFVwSIyxmg4MRsxakfuXHbMZME&s=mGWu0XBCJqG2MI5qPlwIpGbQL5IYe7t5E
> WcvhPYW7Lo&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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