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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: Medication Mention
Date Thu, 19 Dec 2013 16:20:37 GMT
Hi Pan,
Thanks for the useful feedback.  Coming from a new user perspective, how do you think we could
improve the user experience?

-          Add a blub about the pipeline in the documentation [1]

-          Update the default pipeline to contain the DrugNER (smoking status, relation extractor,
coreference, others)?- Drug signatures is probably a pretty common use case...

[1] https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+Component+Use+Guide

From: Pan Teng [mailto:tengpan@udel.edu]
Sent: Thursday, December 19, 2013 2:50 AM
To: user@ctakes.apache.org
Subject: Re: Medication Mention

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<mailto: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<mailto: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<mailto:tengpan@udel.edu>]
Sent: Monday, December 16, 2013 4:07 PM
To: user@ctakes.apache.org<mailto: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:



[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<mailto: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<mailto:tengpan@udel.edu>]
Sent: Monday, December 16, 2013 3:43 PM
To: user@ctakes.apache.org<mailto: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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