it seems to me that we have willing contributors, but no driver for this project. Any ideas?
-NM On Thu, May 8, 2014 at 8:17 PM, Maha Zohbi <[email protected]> wrote: > 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 >>> >> >> >
