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 < [email protected]> 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 > >>> <[email protected]> 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:[email protected]] > >>>>> Sent: Thursday, May 01, 2014 7:41 PM > >>>>> To: [email protected] > >>>>> 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 > >>>> [email protected] > >>>> 617-919-1223 [2] > >> -- > >> Tim Miller > >> Instructor > >> Boston Children's Hospital and Harvard Medical School > >> [email protected] > >> 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 > [email protected] > 617-919-1223 > > -- Ravi Garg 4th Year MSc (hons) Biological Sciences B.E (hons) Computer Science and Engineering BITS Pilani KK Birla Goa Campus
