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From N M <maveric...@gmail.com>
Subject Re: cTAKES API documentation
Date Wed, 14 May 2014 16:22:11 GMT
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 <mahazohbi@gmail.com> wrote:

> 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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