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From Abhishek Raj <abhishe...@iitrpr.ac.in>
Subject Re: API for running ctakes programatically
Date Wed, 18 Jun 2014 15:05:37 GMT
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 <chenpei@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 <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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