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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Identification of prostatectomy
Date Thu, 15 Oct 2015 17:40:12 GMT
Hi Sangram,

I would love to say that I have a simple answer for you, but I don't.  There is an engine
that will attempt to identify events as hedged, hypothetical, actual or generic ... the ContextualModalityAnnotator
in the ctakes-temporal module.  However, it is not in the commonly used pipelines, and I have
no idea how well it works.  It is possible that somebody else out there is using this annotator
to great success or at least knows more about it than I.

Sean

-----Original Message-----
From: Sangram Patil [mailto:sangramp@figmd.com] 
Sent: Thursday, October 15, 2015 12:49 AM
To: dev@ctakes.apache.org
Subject: Re: Identification of prostatectomy

Many thanks, Sean!

I have patient-clinical-notes e.g.

   - 83 y.o. Asian gentleman who is status post a robotic-assisted radical
   prostatectomy in October of 2006 for pathologic stage T2c, Gleason 4+3
   prostate cancer excised with a negative surgical margin but benign glands
   at the margin.
   - The patient is a 73-year-old Caucasian  gentleman who is status post radical
   prostatectomy in 2006.
   - Greater than 30 minutes of face to face discussion time were spent
   discussing the prostate gland, prostate diseases and prostate cancer.  We discussed
   open radical prostatectomy, daVinci prostatectomy, external beam
   radiation, brachytherapy, cryotherapy, androgen deprivation, watchful
   waiting and HIFU.
   - We discussed different treatment options for prostate cancer. We
   discussed non-curative options including active surveillance and hormone
   therapy. We also discussed potentially curative options including surgery
   versus radiation and cryotherapy.

The note gets annotated using clinical pipeline - AggregatePlaintextFastUMLSProcessor.
By searching keyword I can find a treatment. sometimes physician writes about the discussion
and sometime the actual surgery. Now I have problem to finalise if the mentioned procedure/treatment
is really happened or just discussed.  I can't just rely on verb in the sentence.

Your help would help me a lot!


On Fri, Oct 9, 2015 at 6:23 PM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:

> Hi Sangram,
>
> Just fyi, users of some email apps (e.g. Outlook) may not be able to 
> reply to a message with a web address in the title.
>
> Now to your question:
>
> >69 y.o. Caucasian gentleman with a history of prostate cancer s/p 
> >open
> RRP in 9/2005 for a pT2c, GS3+4 prostate cancer excised with a 
> negative margin.
>
> > on what basis I can make out if the patient has underwent 
> > prostatectomy
>
> The output has underlined "RRP" and marked it as a procedure with UMLS 
> CUI
> C0194825 .
> As the author of the question, you probably already know that an rrp 
> is a (radical retropubic) prostatectomy.  However, if you did not then 
> you can see that it is marked in the sentence as a procedure, making 
> it a candidate.  If you visit the UMLS metathesaurus 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts.nlm.nih.gov_metathesaurus.html&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=F_5Xmb5KaG1WtQQR78xx8AleQvJTOqZEeIgwRUewe1w&s=YgPBaqDMDp6zVtBKzAgCjuzCPOnYnXtlv8kqpzRHzac&e=
 and enter the CUI C0194825 .
> The metathesaurus will display (among other things):
> Radical retropubic prostatectomy
> Therapeutic or Preventative Procedure
> Surgery to remove all of the prostate and nearby lymph nodes through 
> an incision in the wall of the abdomen.
>
> If you aren't able to use the metathesaurus then you can apply for a 
> free user license from the nlm: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts.nlm.nih.gov__
> license.html&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=F_5Xmb5KaG1WtQQR78xx8Ale
> QvJTOqZEeIgwRUewe1w&s=njFE-cg3zaLnwHaClL09gNybN1aw91r3TvQpDqi6bHs&e= < 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts.nlm.nih.gov_l
> icense.html&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=f
> s67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=F_5Xmb5KaG1WtQQR78xx8AleQ
> vJTOqZEeIgwRUewe1w&s=DASDSV2lLrnUmIg9Ne7_9y62iMMP0NAuxVNUWpo1_rA&e= >
>
> If you would like to have more information (such as term preferred 
> text listing), please add a jira item as a "nice to have" and maybe 
> somebody will implement it.  It isn't in there now because I didn't 
> want the display to get cluttered.
>
> Sean
>
>
>


--
Sincerely,
Sangram Patil
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