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From Tom Devel <deve...@gmail.com>
Subject Re: Allergy Annotator
Date Fri, 10 Jul 2015 19:44:06 GMT
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.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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