Hi Tom, Just for fun I checked "ctakes-allergy" into sandbox. Great title. While too simple to be really useful, it might serve as a testing point or example for future endeavors.
Sean -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Friday, July 10, 2015 4:21 PM To: dev@ctakes.apache.org Subject: RE: Allergy Annotator 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:deve...@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.fi...@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.dlig...@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 <deve...@gmail.com<mailto: > deve...@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.fi...@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:deve...@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 > > >
