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From Pei Chen <chen...@apache.org>
Subject Re: API for running ctakes programatically
Date Wed, 18 Jun 2014 14:33:48 GMT
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 <vngarla@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 <abhishekrm@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! :)
>>
>>
>

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