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:[email protected]]
Sent: Friday, July 10, 2015 4:12 PM
To: [email protected]
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 <
[email protected]> 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:[email protected]]
> 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 <[email protected]<mailto:
> [email protected]>> 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 <
> [email protected]<mailto:[email protected]
> 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:[email protected]]
> Sent: Friday, July 10, 2015 12:42 PM
> To: [email protected]<mailto:[email protected]>
> 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
>
>
>
