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From Sangram Patil <sangr...@figmd.com>
Subject Re: Identification of prostatectomy
Date Fri, 16 Oct 2015 05:06:52 GMT
Thank you so much, Timothy and Sean!

Will try and update you!

On Fri, Oct 16, 2015 at 12:52 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> 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
>



-- 
** Please include your practice ID in your correspondence.*

Sincerely,

Sangram Patil
Team Lead-Core Dev
Cell: +91 992 293 9497


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