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From "Savova, Guergana" <Guergana.Sav...@childrens.harvard.edu>
Subject RE: Regarding inconsistency in UMLS Dictionary Lookup Annotator
Date Mon, 15 Apr 2013 21:32:38 GMT
Please, check whether you are running the LVG before the named entity recognition module.
--Guergana

From: Deepal Dhariwal [mailto:deepaldhariwal@gmail.com]
Sent: Monday, April 15, 2013 5:16 PM
To: Kim Ebert
Cc: user@ctakes.apache.org; 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<mailto: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<mailto: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<tel: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<mailto: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<tel: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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