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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: Regarding inconsistency in UMLS Dictionary Lookup Annotator
Date Wed, 17 Apr 2013 14:15:53 GMT
Hi Kim,
This actually looks like a pretty good bug fix.
It seems like you already have the code/patch, should we just commit it to trunk once you
verify the fix?

--Pei

From: Kim Ebert [mailto:kim.ebert@perfectsearchcorp.com]
Sent: Monday, April 15, 2013 4:41 PM
To: Deepal Dhariwal
Cc: user@ctakes.apache.org; ctakes-user@incubator.apache.org
Subject: Re: Regarding inconsistency in UMLS Dictionary Lookup Annotator

Hi Deepal,

I have a patch for cTAKES 2.5 to resolve the problem of batch processing returning fewer results
as processing continues due to the permutation list becoming corrupt.

https://issues.apache.org/jira/browse/CTAKES-146

The patch should still apply to ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java

Thanks,


Kim Ebert

1.801.669.7342

Perfect Search Corp

http://www.perfectsearchcorp.com/
On 04/15/2013 01:53 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<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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