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From Pan Teng <teng...@udel.edu>
Subject Re: Medication Mention
Date Thu, 19 Dec 2013 18:59:36 GMT
Hi Pei,

Thank you for your quick reply. From my end, if there can be an example
input, and output, which can utilize all the components in cTAKES will help
a lot. From the output, maybe it's easier to see whether this system can
generate information that useful for my research area, and differentiate
cTAKES from other clinical NLP tools.

Best,
Pan




On Thu, Dec 19, 2013 at 11:20 AM, Chen, Pei
<Pei.Chen@childrens.harvard.edu>wrote:

>  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> 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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