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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: cTAKES API documentation
Date Thu, 15 May 2014 14:43:54 GMT
+1 on a format to make easily editable rather than pdf.
I think Troy/James worked on the cwiki documentation, so perhaps they’ll probably best to
find a good place for this in the comonents guide...

Some additional thoughts though:

1)      It would be nice if this information (Annotator input/output) was in 1 place.
We never really took advantage of the <capabilities><input/><output/></capabilities>
in the UIMA descriptors.  One can update every single desc to better reflect the annotators/pipelines.
 This info can be used to populate the flow chart?

2)      Tim and co. is writing Factory classes[1] to easily wire pipelines together via code.
 We can add the input/output types in the javadoc comments so this info is available right
from the code.  I think this will be a good and clean starting place for new developers in
the future…

[1] http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java

From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
Sent: Thursday, May 15, 2014 4:11 AM
To: 'user@ctakes.apache.org'
Subject: RE: cTAKES API documentation

There were slides created for the very first release of cTAKES that showed something along
these lines. I don’t see it online anymore, but it’s outdated anyway. I’ll look for
a copy and post them somewhere.

I like the PDF but I’d suggest keeping the format as simple as possible to make it easy
to make updates.

Also, I suggest either removing or adding a footnote for those attributes that aren’t set
by a given annotator.  For example, the output of Tokenizer Annotator is shown to be BaseToken,
but because some attributes of BaseToken are listed, someone might wrongly infer that the
Tokenizer sets the values of those attributes, when some of them are actually set by later

It would also be good to list which release of cTAKES it applies to.

-- James

From: N M [mailto:mavericnlp@gmail.com]
Sent: Tuesday, May 06, 2014 4:01 PM
To: user@ctakes.apache.org
Subject: Re: cTAKES API documentation

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?


On Fri, May 2, 2014 at 2:17 PM, ravi garg <ravigarg27@gmail.com<mailto:ravigarg27@gmail.com>>
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

On Fri, May 2, 2014 at 10:07 PM, Miller, Timothy <Timothy.Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harvard.edu>>
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
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:
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:

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:

Hope this helps.


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<mailto:Timothy.Miller@childrens.harvard.edu>>
>>>> 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<mailto:huangxy@cs.wisc.edu>]
>>>>> Sent: Thursday, May 01, 2014 7:41 PM
>>>>> To: user@ctakes.apache.org<mailto: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<mailto:timothy.miller@childrens.harvard.edu>
>>>> 617-919-1223<tel:617-919-1223> [2]
>> --
>> Tim Miller
>> Instructor
>> Boston Children's Hospital and Harvard Medical School
>> timothy.miller@childrens.harvard.edu<mailto:timothy.miller@childrens.harvard.edu>
>> 617-919-1223<tel:617-919-1223>
>> Links:
>> ------
>> [1] http://ctakes.apache.org/apidocs/3.1.1/
>> [2] tel:617-919-1223<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
Boston Children's Hospital and Harvard Medical School

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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