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Posted to user@ctakes.apache.org by Snehal <sn...@gmail.com> on 2013/07/09 09:16:32 UTC
Help configuring ctakes for disease/medication Annotation detection
Hello,
I am trying to configure ctakes - dictionary lookup module using
Uimafit to detect disease/medication given a sample text. When I run
the attached unit test, I am unable to find any annotations. Any idea
what I am missing?
Thanks,
Snehal
Re: Help configuring ctakes for disease/medication Annotation detection
Posted by Snehal <sn...@gmail.com>.
Hello Pei,
With the help of your example I have successfully been to annotate the
text with medication/diseases. Thanks!
Regards,
Snehal
On Tue, Jul 9, 2013 at 10:30 AM, Snehal <sn...@gmail.com> wrote:
> Hi Pei,
>
> Thanks for the reply. What window annotation do you think would
> suffice for just identifying the presence of disease/drug or
> medication keywords? I see that there are Sentence, Segment, Paragraph
> and LookupWindowAnnotation.
>
> Also, I can't find CopyNPChunksToLookupWindowAnnotations class in
> ctakes 3.0.1. Is this added only in 3.1?
>
> Regards,
> Snehal
>
> On Tue, Jul 9, 2013 at 8:07 AM, Chen, Pei
> <Pe...@childrens.harvard.edu> wrote:
>> Hi Snehal,
>>
>>> -----Original Message-----
>>> From: Snehal [mailto:snehal.kumar@gmail.com]
>>> Sent: Tuesday, July 09, 2013 11:00 AM
>>> To: user
>>> Subject: Re: Help configuring ctakes for disease/medication Annotation
>>> detection
>>> Does ctakes require all the different components such as Chunker,POS
>>> tagger etc; for identifying this?
>>
>> The short answer is yes. The longer answer is that the test case desc is configured to use the below Type to constrain the lookup window (which is essentially constrained to Noun Phrases hence the prerequisites).
>> <property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>
>> [Of course, that can be modified/configured for your use case(s).]
>>
>> --Pei
>>
>>
Re: Help configuring ctakes for disease/medication Annotation detection
Posted by Snehal <sn...@gmail.com>.
Hi Pei,
Thanks for the reply. What window annotation do you think would
suffice for just identifying the presence of disease/drug or
medication keywords? I see that there are Sentence, Segment, Paragraph
and LookupWindowAnnotation.
Also, I can't find CopyNPChunksToLookupWindowAnnotations class in
ctakes 3.0.1. Is this added only in 3.1?
Regards,
Snehal
On Tue, Jul 9, 2013 at 8:07 AM, Chen, Pei
<Pe...@childrens.harvard.edu> wrote:
> Hi Snehal,
>
>> -----Original Message-----
>> From: Snehal [mailto:snehal.kumar@gmail.com]
>> Sent: Tuesday, July 09, 2013 11:00 AM
>> To: user
>> Subject: Re: Help configuring ctakes for disease/medication Annotation
>> detection
>> Does ctakes require all the different components such as Chunker,POS
>> tagger etc; for identifying this?
>
> The short answer is yes. The longer answer is that the test case desc is configured to use the below Type to constrain the lookup window (which is essentially constrained to Noun Phrases hence the prerequisites).
> <property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>
> [Of course, that can be modified/configured for your use case(s).]
>
> --Pei
>
>
RE: Help configuring ctakes for disease/medication Annotation
detection
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Hi Snehal,
> -----Original Message-----
> From: Snehal [mailto:snehal.kumar@gmail.com]
> Sent: Tuesday, July 09, 2013 11:00 AM
> To: user
> Subject: Re: Help configuring ctakes for disease/medication Annotation
> detection
> Does ctakes require all the different components such as Chunker,POS
> tagger etc; for identifying this?
The short answer is yes. The longer answer is that the test case desc is configured to use the below Type to constrain the lookup window (which is essentially constrained to Noun Phrases hence the prerequisites).
<property key="windowAnnotations" value="org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation"/>
[Of course, that can be modified/configured for your use case(s).]
--Pei
Re: Help configuring ctakes for disease/medication Annotation detection
Posted by Snehal <sn...@gmail.com>.
Hello Pei,
Thanks for the input. I think I missed the config for Lookup window.
My use case is just for identifying if a text contains disease or drug
mention. Does ctakes require all the different components such as
Chunker,POS tagger etc; for identifying this?
Regards,
Snehal
Snehal
On Tue, Jul 9, 2013 at 7:34 AM, Chen, Pei
<Pe...@childrens.harvard.edu> wrote:
> Hi Snehal,
> The lookup window is most likely empty.
> It looks like the test case is configured to only run the Dictionary Lookup component alone.
> The dictionary look up component is dependent on others such as: SimpleSegment > Sentence Dectector > Tokenizer > POS Tagger > Chunker
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Component+Use+Guide
>
> A recent example:
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventExtractionPipeline.java
>
> I hope that helps.
> --Pei
>
>> -----Original Message-----
>> From: Snehal [mailto:snehal.kumar@gmail.com]
>> Sent: Tuesday, July 09, 2013 3:18 AM
>> To: user
>> Subject: Help configuring ctakes for disease/medication Annotation
>> detection
>>
>> Hello,
>>
>> I am trying to configure ctakes - dictionary lookup module using Uimafit to
>> detect disease/medication given a sample text. When I run the attached unit
>> test, I am unable to find any annotations. Any idea what I am missing?
>>
>> Thanks,
>> Snehal
RE: Help configuring ctakes for disease/medication Annotation
detection
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Hi Snehal,
The lookup window is most likely empty.
It looks like the test case is configured to only run the Dictionary Lookup component alone.
The dictionary look up component is dependent on others such as: SimpleSegment > Sentence Dectector > Tokenizer > POS Tagger > Chunker
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Component+Use+Guide
A recent example:
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventExtractionPipeline.java
I hope that helps.
--Pei
> -----Original Message-----
> From: Snehal [mailto:snehal.kumar@gmail.com]
> Sent: Tuesday, July 09, 2013 3:18 AM
> To: user
> Subject: Help configuring ctakes for disease/medication Annotation
> detection
>
> Hello,
>
> I am trying to configure ctakes - dictionary lookup module using Uimafit to
> detect disease/medication given a sample text. When I run the attached unit
> test, I am unable to find any annotations. Any idea what I am missing?
>
> Thanks,
> Snehal