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From Maha Zohbi <mahazo...@gmail.com>
Subject Re: cTAKES API documentation
Date Fri, 09 May 2014 00:17:32 GMT
Thanks all for your help!


On Wed, May 7, 2014 at 7:00 AM, N M <mavericnlp@gmail.com> 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 <ravigarg27@gmail.com> 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 <
>> 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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