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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Identification of prostatectomy
Date Thu, 15 Oct 2015 19:22:49 GMT
Thanks Tim.  It looks like "generic" does make the attempt, and for most of this it is close.

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.
"assisted" in history for patient
 	Finding
 	 	C1269765 Assisted (qualifier value)
"radical prostatectomy" in history for patient
 	Procedure
 	 	C0194810 Radical prostatectomy
"prostatectomy" in history for patient
 	Procedure
 	 	C0033573 Prostatectomy
"prostate cancer" for patient
 	Disorder
 	 	C0376358 Malignant neoplasm of prostate
 	 	C0600139 Prostate carcinoma
"prostate" for patient
 	Anatomy
 	 	C0033572 Prostate
 	 	C1278980 Entire prostate
"cancer" for patient
 	Disorder
 	 	C0006826 Malignant Neoplasms
 	 	C1306459 Primary malignant neoplasm
"surgical margin" for patient
 	Anatomy
 	 	C0229985 Surgical margins
"surgical" for patient
 	Procedure
 	 	C0543467 Operative Surgical Procedures
"margin" for patient
 	Anatomy
 	 	C0229985 Surgical margins
"glands" for patient
 	Anatomy
 	 	C1285092 Gland
"margin" for patient
 	Anatomy
 	 	C0229985 Surgical margins


The patient is a 73-year-old Caucasian  gentleman who is status post radical prostatectomy
in 2006.
"radical prostatectomy" in history for patient
 	Procedure
 	 	C0194810 Radical prostatectomy
"prostatectomy" in history for patient
 	Procedure
 	 	C0033573 Prostatectomy


Greater than 30 minutes of face to face discussion time were spent discussing the prostate
gland, prostate diseases and prostate cancer.
"face" for patient
 	Anatomy
 	 	C0015450 Face
 	 	C1281591 Entire face
"face" for patient
 	Anatomy
 	 	C0015450 Face
 	 	C1281591 Entire face
"discussion" for patient
 	Procedure
 	 	C0557061 Discussion (procedure)
"prostate gland" for patient
 	Anatomy
 	 	C0033572 Prostate
"prostate" for patient
 	Anatomy
 	 	C0033572 Prostate
 	 	C1278980 Entire prostate
"gland" for patient
 	Anatomy
 	 	C1285092 Gland
"prostate diseases" for patient
 	Disorder
 	 	C0033575 Prostatic Diseases
"prostate" for patient
 	Anatomy
 	 	C1278980 Entire prostate
 	 	C0033572 Prostate
"diseases" for patient
 	Disorder
 	 	C0012634 Disease
"prostate cancer" for patient
 	Disorder
 	 	C0600139 Prostate carcinoma
 	 	C0376358 Malignant neoplasm of prostate
"prostate" for patient
 	Anatomy
 	 	C0033572 Prostate
 	 	C1278980 Entire prostate
"cancer" for patient
 	Disorder
 	 	C1306459 Primary malignant neoplasm
 	 	C0006826 Malignant Neoplasms

We discussed open radical prostatectomy, daVinci prostatectomy, external beam radiation, brachytherapy,
cryotherapy, androgen deprivation, watchful waiting and HIFU.
"radical prostatectomy" generic for patient
 	Procedure
 	 	C0194810 Radical prostatectomy
"prostatectomy" generic for patient
 	Procedure
 	 	C0033573 Prostatectomy
"prostatectomy" for patient
 	Procedure
 	 	C0033573 Prostatectomy
"radiation" generic for patient
 	Procedure
 	 	C1522449 Therapeutic radiology procedure
"brachytherapy" generic for patient
 	Procedure
 	 	C0006098 Brachytherapy
"cryotherapy" generic for patient
 	Procedure
 	 	C0010408 Cryosurgery
 	 	C0010412 Cold Therapy


We discussed different treatment options for prostate cancer.
"treatment" generic for patient
 	Procedure
 	 	C1533734 Administration procedure
 	 	C0087111 Therapeutic procedure
"prostate cancer" generic for patient
 	Disorder
 	 	C0376358 Malignant neoplasm of prostate
 	 	C0600139 Prostate carcinoma
"prostate" for patient
 	Anatomy
 	 	C1278980 Entire prostate
 	 	C0033572 Prostate
"cancer" generic for patient
 	Disorder
 	 	C0006826 Malignant Neoplasms
 	 	C1306459 Primary malignant neoplasm

We discussed non-curative options including active surveillance and hormone therapy.
"active" for patient
 	Drug
 	 	C0718247 Active brand of pseudoephedrine-triprolidine
"hormone therapy" generic for patient
 	Procedure
 	 	C0279025 Endocrine therapy
"therapy" for patient
 	Procedure
 	 	C0087111 Therapeutic procedure

We also discussed potentially curative options including surgery versus radiation and cryotherapy.
"surgery" generic for patient
 	Procedure
 	 	C0543467 Operative Surgical Procedures
"radiation" generic for patient
 	Procedure
 	 	C1522449 Therapeutic radiology procedure
"cryotherapy" generic for patient
 	Procedure
 	 	C0010408 Cryosurgery
 	 	C0010412 Cold Therapy


-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu] 
Sent: Thursday, October 15, 2015 1:45 PM
To: dev@ctakes.apache.org
Subject: Re: Identification of prostatectomy

I think this case might be covered by the "generic" status classifier from the assertion module?
It distinguishes generic mentions of an event from actual mentions (generic covering both
discussions and other things like "she knows chemotherapy causes side effects" where neither
entity is actual yet). That is part of a default pipeline but it is harder than negation or
uncertainty. You can try it and see whether it works well enough on your data to be useful.
Tim

________________________________________
From: Finan, Sean <Sean.Finan@childrens.harvard.edu>
Sent: Thursday, October 15, 2015 1:40 PM
To: dev@ctakes.apache.org
Subject: RE: Identification of prostatectomy

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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