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Posted to user@ctakes.apache.org by Pan Teng <te...@udel.edu> on 2013/12/16 21:42:02 UTC
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
Re: Medication Mention
Posted by Pan Teng <te...@udel.edu>.
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
<Pe...@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 <te...@udel.edu> wrote:
>
> It's working. Thanks Pei.
>
>
>
> Pan
>
>
>
> On Mon, Dec 16, 2013 at 4:09 PM, Chen, Pei <Pe...@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 <Pe...@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
>
>
>
>
>
>
>
RE: Medication Mention
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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 <te...@udel.edu>> wrote:
It's working. Thanks Pei.
Pan
On Mon, Dec 16, 2013 at 4:09 PM, Chen, Pei <Pe...@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<ma...@udel.edu>]
Sent: Monday, December 16, 2013 4:07 PM
To: user@ctakes.apache.org<ma...@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 <Pe...@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<ma...@udel.edu>]
Sent: Monday, December 16, 2013 3:43 PM
To: user@ctakes.apache.org<ma...@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
Re: Medication Mention
Posted by Pan Teng <te...@udel.edu>.
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 <te...@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
>>
>>
>>
>
>
Re: Medication Mention
Posted by Pan Teng <te...@udel.edu>.
It's working. Thanks Pei.
Pan
On Mon, Dec 16, 2013 at 4:09 PM, Chen, Pei
<Pe...@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 <Pe...@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
>
>
>
RE: Medication Mention
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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:
[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 <Pe...@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<ma...@udel.edu>]
Sent: Monday, December 16, 2013 3:43 PM
To: user@ctakes.apache.org<ma...@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
Re: Medication Mention
Posted by Pan Teng <te...@udel.edu>.
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
<Pe...@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
>
RE: Medication Mention
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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