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From Pan Teng <teng...@udel.edu>
Subject Re: Medication Mention
Date Thu, 19 Dec 2013 07:49:49 GMT
Hi Pei,

Just wondering, if I didn't see this in one of your slides of presentation,
I wouldn't know that this drug mention annotator is not included in the
AggregateUMLSPlaintextprocessor.xml. How can I know that which part of
cTAKES is working, what else is not included here in
AggregateUMLSPlaintextprocessor.xml but should be working?

Thanks,
Pan


On Mon, Dec 16, 2013 at 4:20 PM, Pan Teng <tengpan@udel.edu> wrote:

> It's working. Thanks Pei.
>
> Pan
>
>
> On Mon, Dec 16, 2013 at 4:09 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu
> > wrote:
>
>>   If you have DictionaryLookupAnnotatorDB defined earlier, try the
>> DictionaryLookupAnnotatorDB.
>>
>>         <node> DictionaryLookupAnnotatorDB</node>
>>
>>         <node>DrugMentionAnnotator</node>
>>
>>
>>
>>
>>
>> *From:* Pan Teng [mailto:tengpan@udel.edu]
>> *Sent:* Monday, December 16, 2013 4:07 PM
>> *To:* user@ctakes.apache.org
>> *Subject:* Re: Medication Mention
>>
>>
>>
>> Hi Pei,
>>
>>
>>
>> I was using the default AggregateUMLSPlaintextprocessor.xml.
>>
>>
>>
>> I have <node>DictionaryLookupAnnotatorDB</node> instead of
>>
>>        <node>DrugMentionAnnotator</node> you mentioned.
>>
>> I edited the AggregateUMLSPlaintextprocessor.xml as you said, then I got
>> the error like:
>>
>>
>>
>> [image: Inline image 1]
>>
>>
>>
>> The attached is the xml file after I added the DrugNER just now.
>>
>>
>>
>> Many thanks for your quick reply.
>>
>>
>>
>> --Pan
>>
>>
>>
>> On Mon, Dec 16, 2013 at 3:48 PM, Chen, Pei <
>> Pei.Chen@childrens.harvard.edu> wrote:
>>
>> Hi Pan,
>>
>> Could you attach the pipeline configuration (is it
>> DefaultAggregateUMLSPlaintextprocessor.xml)?
>>
>> In particular,
>>
>> Do you have the DrugNER (for the drug signatures) in your pipeline?
>>
>>     <delegateAnalysisEngine key=*"DrugMentionAnnotator"*>
>>
>>       <import location=
>> *"../../../ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml"*
>> />
>>
>>     </delegateAnalysisEngine>
>>
>>
>>
>> …
>>
>>         <node>DictionaryLookupAnnotator</node>
>>
>>         <node>DrugMentionAnnotator</node>
>>
>> …
>>
>> --Pei
>>
>>
>>
>> *From:* Pan Teng [mailto:tengpan@udel.edu]
>> *Sent:* Monday, December 16, 2013 3:43 PM
>> *To:* user@ctakes.apache.org
>> *Subject:* Medication Mention
>>
>>
>>
>> Hi cTAKES community,
>>
>>
>>
>> I saw in one of the slides from your presentation saying that, query like
>> "The patient took aspirin 325 mg for knee pain."  will have annotation
>> like <edu.mayo.bmi.uima.core.type.refsem.MedicationStrength
>>     value number = “325” unit = “mg”>
>>
>> <edu.mayo.bmi.uima.core.type.refsem.MedicationStatusChange
>>     value="noChange" />
>>
>>
>>
>> But when I ran this, I only got
>>
>>
>>
>> medicationStrength = <null>, medicationStatusChange = <null>
>>
>>
>>
>> Is the annotation for medication working properly?
>>
>> I'm not sure what's wrong here. Any clues?
>>
>>
>>
>> Best,
>>
>> Pan
>>
>>
>>
>
>

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