Thanks all for your help!
On Wed, May 7, 2014 at 7:00 AM, N M <[email protected]> wrote: > Hi, > > Documentation which I was hoping to find as a user (hopefully eventually > developer) of cTAKES, was a detailed description of each component (or > analysis engine) and their interplay. As I've been looking at the cTAKES > source code, I've been creating a chart for each pipeline that I've > analyzed, hoping to essentially create a more useful component library than > the one available at > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Component+Use+Guide(a > "developer version" of this, if you will). > > I've attached a pdf example of one of my personal note charts I've been > working on, this one is specific to the UMLS plaintext aggregate AE. My > idea is to have some sort of diagram for each pipeline that I can refer to, > so that when I need to customize things in the future, I have a pretty good > idea of where to go. I think it is important to chart inputs and output > types especially. > > Has anyone written a UIMA library to automatically document these kinds of > things for UIMA components? running something akin to one would save a lot > of time and effort, and would be much more maintainable than manually > created charts. (of course, the inputs and outputs would have to be noted > in the xml files, which doesn't seem to be the case for many of the AE's). > > Looking at the previous discussions (notably the one regarding lvg > entries), it seems to me that having a chart or other type of documentation > which lists what types come out of and go into each component would go a > long ways. > > Does anyone know if anything similar exists? > > Thanks. > > > > > On Fri, May 2, 2014 at 2:17 PM, ravi garg <[email protected]> wrote: > >> 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 >> > >
