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From Kim Ebert <kim.eb...@perfectsearchcorp.com>
Subject Re: Regarding inconsistency in UMLS Dictionary Lookup Annotator
Date Mon, 15 Apr 2013 20:40:10 GMT
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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