ctakes-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Karthik Sarma <ksa...@ksarma.com>
Subject Re: Regarding inconsistency in UMLS Dictionary Lookup Annotator
Date Tue, 16 Apr 2013 01:03:02 GMT
Hmm that shouldnt really matter in these cases so long as the runs were
consistent wrt ordering

On Monday, April 15, 2013, Savova, Guergana wrote:

>  Please, check whether you are running the LVG before the named entity
> recognition module. ****
>
> --Guergana****
>
> ** **
>
> *From:* Deepal Dhariwal [mailto:deepaldhariwal@gmail.com<javascript:_e({}, 'cvml',
'deepaldhariwal@gmail.com');>]
>
> *Sent:* Monday, April 15, 2013 5:16 PM
> *To:* Kim Ebert
> *Cc:* user@ctakes.apache.org <javascript:_e({}, 'cvml',
> 'user@ctakes.apache.org');>; ctakes-user@incubator.apache.org<javascript:_e({},
'cvml', 'ctakes-user@incubator.apache.org');>
> *Subject:* Re: Regarding inconsistency in UMLS Dictionary Lookup Annotator
> ****
>
> ** **
>
> 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****
>
> ** **
>
>

-- 
Sent from Gmail Mobile

Mime
View raw message