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From ravi garg <ravigar...@gmail.com>
Subject Re: cTAKES API documentation
Date Fri, 02 May 2014 18:17:13 GMT
Hi Xiayuan,

I hope this [1]  will be of help to you.

[1]
https://github.com/ravigarg27/phenotips/blob/master/components/ctakes-service/src/main/java/edu/toronto/cs/phenotips/ctakes/AbstractScriptService.java

Regards,
Ravi


On Fri, May 2, 2014 at 10:07 PM, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> 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
>
>


-- 
Ravi Garg
4th Year
MSc (hons) Biological Sciences
B.E (hons) Computer Science and Engineering
BITS Pilani KK Birla Goa Campus

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