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:[email protected]]
Sent: Thursday, October 15, 2015 1:45 PM
To: [email protected]
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 <[email protected]>
Sent: Thursday, October 15, 2015 1:40 PM
To: [email protected]
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:[email protected]]
Sent: Thursday, October 15, 2015 12:49 AM
To: [email protected]
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 < [email protected]>
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
