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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: cTAKES API documentation
Date Fri, 02 May 2014 16:37:59 GMT
James posted the links to the API docs earlier, but I suspect you may
find examples more helpful.

If you look at the classes under
/ctakes-clinical-pipeline/org.apache.ctakes.clinicalpipeline.runtime,
you will see how to instantiate the default pipelines from within
UimaFit using the xml descriptors.  You can override
BagOfAnnotationsGenerator with your own extractInformation() method and
do whatever you like for each annotation, or you can just copy the
layout to do something you like.

Alternatively, if you want to build your own pipelines programatically,
I would look at some of the pipelines in the ctakes-temporal project:
/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
if you aren't up to date on trunk (i.e. you are working off of a
release), then look at the most recent version in svn:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup

Finally, there is work-in-progress to define factory methods for getting
commonly used pipelines, not ready for primetime but may give you some
more examples of how pipelines can be put together:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java?view=markup

Hope this helps.

Tim

On 05/02/2014 12:16 PM, Xiayuan Huang wrote:
> Actually I am looking for some API documentation like how to use and 
> code with ctakes pipelines. Can anyone share the experience how do you 
> write codes with some pipelines, (maybe in JAVA or else).
>
> Thanks,
> Xiayuan
>
>
> On 2014-05-02 10:55, Miller, Timothy wrote:
>> Yes Pei, thanks, though now that I see it I'm not as sure that it
>> will be useful to Maha and Xiayuan.
>>  Tim
>>
>> On 05/02/2014 11:17 AM, Pei Chen wrote:
>>
>>> Tim,
>>> Do you mean:
>>>
>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>>> [3]
>>>
>>> ?
>>>
>>> On Fri, May 2, 2014 at 11:14 AM, Miller, Timothy
>>> <Timothy.Miller@childrens.harvard.edu> wrote:
>>>
>>>> Another resource that may be more useful for many use cases is the
>>>> type
>>>> system documentation. I seem to have lost that link -- can anyone
>>>> please
>>>> chime in with it?
>>>>
>>>> On 05/02/2014 11:05 AM, Masanz, James J. wrote:
>>>>> Try
>>>>>
>>>>> http://ctakes.apache.org/apidocs/3.1.1/ [1]
>>>>>
>>>>> -- James
>>>>>
>>>>> -----Original Message-----
>>>>> From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu]
>>>>> Sent: Thursday, May 01, 2014 7:41 PM
>>>>> To: user@ctakes.apache.org
>>>>> Cc: Maha Zohbi
>>>>> Subject: Re: cTAKES API documentation
>>>>>
>>>>> Yes, same question. I have been looking for API or
>>>> documentation for
>>>>> long. Could some one help guide to it?
>>>>>
>>>>> Thanks,
>>>>> Xiayuan
>>>>>
>>>>> On 2014-05-01 18:53, Maha Zohbi wrote:
>>>>>> Hi,
>>>>>>
>>>>>> We are looking to developing an application that processes
>>>>>> unstructured medical data and feeds it into a decision support
>>>> system.
>>>>>> To do that we will use cTAKES. We downloaded the binary and
>>>> followed
>>>>>> the user guide. However, I couldn't find any API
>>>> documentation.
>>>>>> Can anyone point me to API documentation for cTAKES or a
>>>> samples
>>>>>> guide to use the API?
>>>>>>
>>>>>> Thanks
>>>> --
>>>> Tim Miller
>>>> Instructor
>>>> Boston Children's Hospital and Harvard Medical School
>>>> timothy.miller@childrens.harvard.edu
>>>> 617-919-1223 [2]
>> --
>> Tim Miller
>> Instructor
>> Boston Children's Hospital and Harvard Medical School
>> timothy.miller@childrens.harvard.edu
>> 617-919-1223
>>
>>
>> Links:
>> ------
>> [1] http://ctakes.apache.org/apidocs/3.1.1/
>> [2] tel:617-919-1223
>> [3]
>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml

-- 
Tim Miller
Instructor
Boston Children's Hospital and Harvard Medical School
timothy.miller@childrens.harvard.edu
617-919-1223


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