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Posted to user@ctakes.apache.org by Abhishek Raj <ab...@iitrpr.ac.in> on 2014/06/18 07:33:47 UTC
API for running ctakes programatically
Hello. I have been looking for a way to run ctakes programatically to
annotate large number of documents and extract those annotations. I haven't
come across any docs so far which explains how to do that. If someone could
throw some light on this issue, it'd be great. Thanks! :)
Re: API for running ctakes programatically
Posted by Abhishek Raj <ab...@iitrpr.ac.in>.
There's one more little thing that I needed advice on. I am annotating
clinical documents to find out Disorder Mentions in the document. I am
aware that ctakes does that to some extent. What would be the best way to
find Disorder Mentions in clinical documents? I am currently using the
AggregatePlainTextUMLSProcessor for the same. Is there any other analysis
engine that does the job better? How can I get more accurate annotations
for Disorder Mentions in the clinical documents? Thanks! :)
On Wed, Jun 18, 2014 at 8:35 PM, Abhishek Raj <ab...@iitrpr.ac.in>
wrote:
> Thanks a lot for your replies. CPE did the job for me. I used it with the
> "test_plaintext.xml" CPE descriptor and "AggregatePlainTextUmlsProcessor"
> as the Analysis Engine. Gave the path to input directory and gave a custom
> output directory for writing CAS to XML file and that did it for me! Now I
> have the annotation for each input file stored in an XML file in the output
> directory. :)
>
>
> On Wed, Jun 18, 2014 at 8:03 PM, Pei Chen <ch...@apache.org> wrote:
>
>> Also check out the main class in:
>>
>> https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
>> It uses uimaFIT style to programmatically wire up a pipeline and one can
>> also use uimaFIT to access the Annotations (TypeSystem).
>>
>> --Pei
>>
>>
>> On Wed, Jun 18, 2014 at 10:16 AM, vijay garla <vn...@gmail.com> wrote:
>>
>>> To Annotate:
>>> If you have a CPE, and all the components in your pipeline are
>>> threadsafe (i.e. drop LVG from your pipeline), you can increase the threads
>>> in the cpe config
>>> You can use this class: org.apache.ctakes.ytex.tools.RunCPE to run a
>>> cpe from the command line/script
>>>
>>> Alternatively, run multiple CPE's in parallel (they need to be
>>> processing different subsets of the corpus)
>>>
>>> To extract annotations:
>>> Add the YTEX DBConsumer to store the annotations in a database (see
>>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.2+-+YTEX+DBConsumer
>>> )
>>> Make sure you configure 'types to ignore' - you don't want to store
>>> annotations for punctuation.
>>>
>>> You can add the DBConsumer to any pipeline/CPE - you don't need any
>>> other YTEX components (however, you do have to set up a database).
>>>
>>>
>>>
>>>
>>> On Wed, Jun 18, 2014 at 4:56 AM, Richard Eckart de Castilho <
>>> rec@apache.org> wrote:
>>>
>>>> A Groovy script has been mentioned on the developers list that
>>>> illustrates how to use uimaFIT to compose and run a cTAKES pipeline. [1]
>>>>
>>>> I do not know if these scripts are only in SVN or if they are (planned
>>>> to) be part of a release or of some documentation.
>>>>
>>>> Cheers,
>>>>
>>>> -- Richard
>>>>
>>>> [1]
>>>> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201312.mbox/%3C996FC801C05DF64A84246A106FACACD021A0DA@MSGPEXCHA08A.mfad.mfroot.org%3E
>>>>
>>>> On 18.06.2014, at 07:33, Abhishek Raj <ab...@iitrpr.ac.in> wrote:
>>>>
>>>> > Hello. I have been looking for a way to run ctakes programatically to
>>>> annotate large number of documents and extract those annotations. I haven't
>>>> come across any docs so far which explains how to do that. If someone could
>>>> throw some light on this issue, it'd be great. Thanks! :)
>>>>
>>>>
>>>
>>
>
Re: API for running ctakes programatically
Posted by Abhishek Raj <ab...@iitrpr.ac.in>.
Thanks a lot for your replies. CPE did the job for me. I used it with the
"test_plaintext.xml" CPE descriptor and "AggregatePlainTextUmlsProcessor"
as the Analysis Engine. Gave the path to input directory and gave a custom
output directory for writing CAS to XML file and that did it for me! Now I
have the annotation for each input file stored in an XML file in the output
directory. :)
On Wed, Jun 18, 2014 at 8:03 PM, Pei Chen <ch...@apache.org> wrote:
> Also check out the main class in:
>
> https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
> It uses uimaFIT style to programmatically wire up a pipeline and one can
> also use uimaFIT to access the Annotations (TypeSystem).
>
> --Pei
>
>
> On Wed, Jun 18, 2014 at 10:16 AM, vijay garla <vn...@gmail.com> wrote:
>
>> To Annotate:
>> If you have a CPE, and all the components in your pipeline are threadsafe
>> (i.e. drop LVG from your pipeline), you can increase the threads in the cpe
>> config
>> You can use this class: org.apache.ctakes.ytex.tools.RunCPE to run a cpe
>> from the command line/script
>>
>> Alternatively, run multiple CPE's in parallel (they need to be processing
>> different subsets of the corpus)
>>
>> To extract annotations:
>> Add the YTEX DBConsumer to store the annotations in a database (see
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.2+-+YTEX+DBConsumer
>> )
>> Make sure you configure 'types to ignore' - you don't want to store
>> annotations for punctuation.
>>
>> You can add the DBConsumer to any pipeline/CPE - you don't need any other
>> YTEX components (however, you do have to set up a database).
>>
>>
>>
>>
>> On Wed, Jun 18, 2014 at 4:56 AM, Richard Eckart de Castilho <
>> rec@apache.org> wrote:
>>
>>> A Groovy script has been mentioned on the developers list that
>>> illustrates how to use uimaFIT to compose and run a cTAKES pipeline. [1]
>>>
>>> I do not know if these scripts are only in SVN or if they are (planned
>>> to) be part of a release or of some documentation.
>>>
>>> Cheers,
>>>
>>> -- Richard
>>>
>>> [1]
>>> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201312.mbox/%3C996FC801C05DF64A84246A106FACACD021A0DA@MSGPEXCHA08A.mfad.mfroot.org%3E
>>>
>>> On 18.06.2014, at 07:33, Abhishek Raj <ab...@iitrpr.ac.in> wrote:
>>>
>>> > Hello. I have been looking for a way to run ctakes programatically to
>>> annotate large number of documents and extract those annotations. I haven't
>>> come across any docs so far which explains how to do that. If someone could
>>> throw some light on this issue, it'd be great. Thanks! :)
>>>
>>>
>>
>
Re: API for running ctakes programatically
Posted by Pei Chen <ch...@apache.org>.
Also check out the main class in:
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
It uses uimaFIT style to programmatically wire up a pipeline and one can
also use uimaFIT to access the Annotations (TypeSystem).
--Pei
On Wed, Jun 18, 2014 at 10:16 AM, vijay garla <vn...@gmail.com> wrote:
> To Annotate:
> If you have a CPE, and all the components in your pipeline are threadsafe
> (i.e. drop LVG from your pipeline), you can increase the threads in the cpe
> config
> You can use this class: org.apache.ctakes.ytex.tools.RunCPE to run a cpe
> from the command line/script
>
> Alternatively, run multiple CPE's in parallel (they need to be processing
> different subsets of the corpus)
>
> To extract annotations:
> Add the YTEX DBConsumer to store the annotations in a database (see
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.2+-+YTEX+DBConsumer
> )
> Make sure you configure 'types to ignore' - you don't want to store
> annotations for punctuation.
>
> You can add the DBConsumer to any pipeline/CPE - you don't need any other
> YTEX components (however, you do have to set up a database).
>
>
>
>
> On Wed, Jun 18, 2014 at 4:56 AM, Richard Eckart de Castilho <
> rec@apache.org> wrote:
>
>> A Groovy script has been mentioned on the developers list that
>> illustrates how to use uimaFIT to compose and run a cTAKES pipeline. [1]
>>
>> I do not know if these scripts are only in SVN or if they are (planned
>> to) be part of a release or of some documentation.
>>
>> Cheers,
>>
>> -- Richard
>>
>> [1]
>> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201312.mbox/%3C996FC801C05DF64A84246A106FACACD021A0DA@MSGPEXCHA08A.mfad.mfroot.org%3E
>>
>> On 18.06.2014, at 07:33, Abhishek Raj <ab...@iitrpr.ac.in> wrote:
>>
>> > Hello. I have been looking for a way to run ctakes programatically to
>> annotate large number of documents and extract those annotations. I haven't
>> come across any docs so far which explains how to do that. If someone could
>> throw some light on this issue, it'd be great. Thanks! :)
>>
>>
>
Re: API for running ctakes programatically
Posted by vijay garla <vn...@gmail.com>.
To Annotate:
If you have a CPE, and all the components in your pipeline are threadsafe
(i.e. drop LVG from your pipeline), you can increase the threads in the cpe
config
You can use this class: org.apache.ctakes.ytex.tools.RunCPE to run a cpe
from the command line/script
Alternatively, run multiple CPE's in parallel (they need to be processing
different subsets of the corpus)
To extract annotations:
Add the YTEX DBConsumer to store the annotations in a database (see
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.2+-+YTEX+DBConsumer
)
Make sure you configure 'types to ignore' - you don't want to store
annotations for punctuation.
You can add the DBConsumer to any pipeline/CPE - you don't need any other
YTEX components (however, you do have to set up a database).
On Wed, Jun 18, 2014 at 4:56 AM, Richard Eckart de Castilho <re...@apache.org>
wrote:
> A Groovy script has been mentioned on the developers list that illustrates
> how to use uimaFIT to compose and run a cTAKES pipeline. [1]
>
> I do not know if these scripts are only in SVN or if they are (planned to)
> be part of a release or of some documentation.
>
> Cheers,
>
> -- Richard
>
> [1]
> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201312.mbox/%3C996FC801C05DF64A84246A106FACACD021A0DA@MSGPEXCHA08A.mfad.mfroot.org%3E
>
> On 18.06.2014, at 07:33, Abhishek Raj <ab...@iitrpr.ac.in> wrote:
>
> > Hello. I have been looking for a way to run ctakes programatically to
> annotate large number of documents and extract those annotations. I haven't
> come across any docs so far which explains how to do that. If someone could
> throw some light on this issue, it'd be great. Thanks! :)
>
>
Re: API for running ctakes programatically
Posted by Richard Eckart de Castilho <re...@apache.org>.
A Groovy script has been mentioned on the developers list that illustrates how to use uimaFIT to compose and run a cTAKES pipeline. [1]
I do not know if these scripts are only in SVN or if they are (planned to) be part of a release or of some documentation.
Cheers,
-- Richard
[1] http://mail-archives.apache.org/mod_mbox/ctakes-dev/201312.mbox/%3C996FC801C05DF64A84246A106FACACD021A0DA@MSGPEXCHA08A.mfad.mfroot.org%3E
On 18.06.2014, at 07:33, Abhishek Raj <ab...@iitrpr.ac.in> wrote:
> Hello. I have been looking for a way to run ctakes programatically to annotate large number of documents and extract those annotations. I haven't come across any docs so far which explains how to do that. If someone could throw some light on this issue, it'd be great. Thanks! :)