Return-Path: X-Original-To: apmail-ctakes-user-archive@www.apache.org Delivered-To: apmail-ctakes-user-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id D35D110A8A for ; Tue, 16 Apr 2013 02:53:11 +0000 (UTC) Received: (qmail 35943 invoked by uid 500); 16 Apr 2013 02:53:11 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 35920 invoked by uid 500); 16 Apr 2013 02:53:11 -0000 Mailing-List: contact user-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: user@ctakes.apache.org Delivered-To: mailing list user@ctakes.apache.org Delivered-To: moderator for user@ctakes.apache.org Received: (qmail 62961 invoked by uid 500); 16 Apr 2013 00:24:55 -0000 Delivered-To: apmail-incubator-ctakes-user@incubator.apache.org X-ASF-Spam-Status: No, hits=1.5 required=5.0 tests=HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (athena.apache.org: domain of deepaldhariwal@gmail.com designates 209.85.223.180 as permitted sender) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:x-received:in-reply-to:references:date:message-id :subject:from:to:cc:content-type; bh=o/V/6vtBpOe65lyHyhX8jYis/POyI3iWY+87Kn9WlfU=; b=GcIuPpX5ucIbrlAIrTzktw6yaueGAVRDiv0aGjxXcsqAbDeB+smbA39hoU6W+qgEnd JgJlQfDNHjzjItNz71vRbszIso7rTv2D1eO4URBHi4Sc+RTtT+XfbIPirVNXJINHlcbj nGFI0x9TvtRkIIgofJT3HA9psVYDfXqNYfyT5lNjdjlGVw7ejl+xzNa9qaaiCh+PXfWq sJEI395VaaYPGFx/8A1NiIsCgi6jIOWAXakMR7mCH8ClIXZQ0yVf+QCz68ho9wG285VT gOJhFKYio0TJtKr65E9dXfXjOU3RUTk6O2KSzsp5eVPDMHW+nheEt5xNLfq+x8/bGNx1 LI9w== MIME-Version: 1.0 X-Received: by 10.50.128.47 with SMTP id nl15mr61044igb.5.1366071870654; Mon, 15 Apr 2013 17:24:30 -0700 (PDT) In-Reply-To: <516C65EA.2000307@perfectsearchcorp.com> References: <516C55A7.8000502@perfectsearchcorp.com> <516C5770.6010801@perfectsearchcorp.com> <516C65EA.2000307@perfectsearchcorp.com> Date: Mon, 15 Apr 2013 20:24:30 -0400 Message-ID: Subject: Re: Regarding inconsistency in UMLS Dictionary Lookup Annotator From: Deepal Dhariwal To: Kim Ebert Cc: user@ctakes.apache.org, ctakes-user@incubator.apache.org Content-Type: multipart/alternative; boundary=089e013a286a96909104da6f6404 X-Virus-Checked: Checked by ClamAV on apache.org --089e013a286a96909104da6f6404 Content-Type: text/plain; charset=ISO-8859-1 Hello Kim, Thanks for your detailed response. I'll try processing individual records and see if the reason for the canonical forms not getting detected is also batch processing. Regards Deepal Dhariwal On Mon, Apr 15, 2013 at 4:41 PM, Kim Ebert wrote: > To see if batch processing is the culprit, please check by running an > individual record through a process after restarting that process. If the > records are identified, then it would be a problem of batch processing. > > > Thanks, > > Kim Ebert1.801.669.7342 > Perfect Search Corphttp://www.perfectsearchcorp.com/ > > On 04/15/2013 02:27 PM, Deepal Dhariwal wrote: > > Also I found that in few records canonical forms of words were not > annotated. For instance diabetes mellitus is recognized as a clinical > concept , however diabetic is not recognized. Similarly catheterrization is > annotated as medical concept however catheterized is not considered valid. > > Attached herewith are screenshots for the same. Kindly let me know is > this also related to batch processing or is this a limitation of cTAKES > Aggregate UMLS Document Processor. > > Thanks > Deepal Dhariwal > > On Mon, Apr 15, 2013 at 3:53 PM, Deepal Dhariwal > wrote: > >> Hello Kim, >> >> Yeah when I processed record individually blood pressure was annotated >> as a medical concept. Can you kindly explain the reason behind this >> difference in behavior. >> >> Thanks so much. >> >> Regards >> Deepal Dhariwal >> >> >> >> >> On Mon, Apr 15, 2013 at 3:39 PM, Kim Ebert < >> kim.ebert@perfectsearchcorp.com> wrote: >> >>> Hi Deepal, >>> >>> Trying running the records individually and see if it identifies the >>> terms correctly; if so I may have an idea of the problem. >>> >>> Thanks, >>> >>> Kim Ebert1.801.669.7342 >>> Perfect Search Corphttp://www.perfectsearchcorp.com/ >>> >>> On 04/15/2013 01:36 PM, Deepal Dhariwal wrote: >>> >>> Hello Kim, >>> >>> The records were processed in a batch using UIMA Collection processing >>> Engine. >>> The parameters for UIMA CPE were as follows: >>> Descriptor: UIMA File System Collection Reader >>> Analysis Engine: cTAKES Aggregate UMLS Plaintext Processor >>> CAS Consumer: XMI Writer CAS Consumer >>> >>> Thanks >>> Deepal Dhariwal >>> >>> >>> On Mon, Apr 15, 2013 at 3:31 PM, Kim Ebert < >>> kim.ebert@perfectsearchcorp.com> wrote: >>> >>>> Hi Deepal, >>>> >>>> Was either record processed in a batch of records? Or where they >>>> processed as individual records? >>>> >>>> Kim Ebert >>>> 1.801.669.7342 >>>> Perfect Search Corp >>>> http://www.perfectsearchcorp.com/ >>>> >>>> On 04/15/2013 12:49 PM, Deepal Dhariwal wrote: >>>> > Hello all, >>>> > >>>> > I have 2 medical records with the following content: >>>> > >>>> > Record 1 : >>>> > He went to the hospital Emergency Room where his blood pressure was >>>> > 120 / 80 , heart rate 94. >>>> > >>>> > Record 2: >>>> > Weight 197 lbs, up to 6 lbs, blood pressure 128/88, heart rate 70 . >>>> > >>>> > In the first record blood pressure is getting annotated as a Clinical >>>> > Entity Mention and a Medical Concept while in second record blood >>>> > pressure is not getting annotated as a clinical entity. >>>> > >>>> > Could someone shed some light on why the difference in behavior ? I >>>> > have attached the screenshots for reference. >>>> > >>>> > Regards >>>> > Deepal Dhariwal >>>> >>>> >>> >>> >> > > --089e013a286a96909104da6f6404 Content-Type: text/html; charset=ISO-8859-1 Hello Kim,

Thanks for your detailed response. I'll try processing individual records and see if the reason for the canonical forms not getting detected is also batch processing.

Regards
Deepal Dhariwal

On Mon, Apr 15, 2013 at 4:41 PM, Kim Ebert <kim.ebert@perfectsearchcorp.com> wrote:
To see if batch processing is the culprit, please check by running an individual record through a process after restarting that process. If the records are identified, then it would be a problem of batch processing.


Thanks,

Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 04/15/2013 02:27 PM, Deepal Dhariwal wrote:
Also I found that in few records canonical forms of words were not annotated. For instance diabetes mellitus is recognized as a clinical concept , however diabetic is not recognized. Similarly catheterrization is annotated as medical concept however catheterized is not considered valid.

Attached herewith are screenshots for the same. Kindly let me know is this also related to batch processing or is this a limitation of cTAKES Aggregate UMLS Document Processor.

Thanks
Deepal Dhariwal

On Mon, Apr 15, 2013 at 3:53 PM, Deepal Dhariwal <deepaldhariwal@gmail.com> wrote:
Hello Kim,

Yeah when I processed record individually blood pressure was annotated as a medical concept. Can you kindly explain the reason behind this difference in behavior.

Thanks so much.

Regards
Deepal Dhariwal




On Mon, Apr 15, 2013 at 3:39 PM, Kim Ebert <kim.ebert@perfectsearchcorp.com> wrote:
Hi Deepal,

Trying running the records individually and see if it identifies the terms correctly; if so I may have an idea of the problem.

Thanks, 

Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 04/15/2013 01:36 PM, Deepal Dhariwal wrote:
Hello Kim,

The records were processed in a batch using UIMA Collection processing Engine.
The parameters for UIMA CPE were as follows:
Descriptor: UIMA File System Collection Reader
Analysis Engine: cTAKES Aggregate UMLS Plaintext Processor
CAS Consumer: XMI Writer CAS Consumer

Thanks
Deepal Dhariwal


On Mon, Apr 15, 2013 at 3:31 PM, Kim Ebert <kim.ebert@perfectsearchcorp.com> wrote:
Hi Deepal,

Was either record processed in a batch of records? Or where they
processed as individual records?

Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/

On 04/15/2013 12:49 PM, Deepal Dhariwal wrote:
> Hello all,
>
> I have 2 medical records with the following content:
>
> Record 1 :
> He went to the hospital Emergency Room where his blood pressure was
> 120 / 80 , heart rate 94.
>
> Record 2:
> Weight 197 lbs, up to 6 lbs, blood pressure 128/88, heart rate 70 .
>
> In the first record blood pressure is getting annotated as a Clinical
> Entity Mention and a Medical Concept while in second record blood
> pressure is not getting annotated as a clinical entity.
>
> Could someone shed some light on why the difference in behavior ? I
> have attached the screenshots for reference.
>
> Regards
> Deepal Dhariwal







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