Thank you so much, Timothy and Sean! Will try and update you!
On Fri, Oct 16, 2015 at 12:52 AM, Finan, Sean < sean.fi...@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.mil...@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.fi...@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:sangr...@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.fi...@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 figmd.com <http://www.figmd.com/> CONFIDENTIALITY NOTICE <http://www.figmd.com/terms/>
