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From "Hochheiser, Harry Stewart" <har...@pitt.edu>
Subject Re: DeepPheno: guidance on CTakes
Date Sat, 28 Jun 2014 17:38:07 GMT

Following up on these examples, I think I’m still needing a bit of additional guidance.

Specifically, I’m wondering if there’s a some sort of “idiot’s guide to creating new
cTAKES annotators”. Having installed cTAKES and run some of the canned pipelines, I wrote
some very simple code to do some basic extensions as needed for my work. However, I got hung
up on trying to tie the descriptors for the types and annotator files together.

I’ve tried copying and modifying of the existing cTAKES projects, but this doesn’t seem
to work - the JCasGen output doesn’t go where it should, the CVD can’t find the annotator
files, etc.    It’s clear that I’m mission something, but I don’t know what it is. I
was able to get comparable code running in bare UIMA in ~ 15 minutes, but I’d like to build
off of cTAKES output.

 Are there any documents on how to get started?  If not, do you have any suggestions? I’d
be happy to try to write up an intro guide if I could get something to work, but I’m pretty
stuck right now. 



On Jun 27, 2014, at 11:35 AM, Chen, Pei <Pei.Chen@childrens.harvard.edu> wrote:

> Thanks.
> Feel free to add/modify the examples... I just took few mins to create those... 
> Back to working on the upcoming release for me now.
>> -----Original Message-----
>> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
>> Sent: Friday, June 27, 2014 11:33 AM
>> To: dev@ctakes.apache.org
>> Subject: RE: DeepPheno: guidance on CTakes
>> Hi Pei,
>> Nice examples.  The pipeline builder could be simpler (divvied), but they
>> shouldn't leave anybody confused.
>> +1 for the uimafit annotations!
>> -----Original Message-----
>> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
>> Sent: Friday, June 27, 2014 11:11 AM
>> To: Hochheiser, Harry Stewart; dev@ctakes.apache.org
>> Subject: RE: DeepPheno: guidance on CTakes
>> +dev
>> Harry,
>> I've just checked in some two example java classes [1] that should make life a
>> lot easier for developers to create and add new cTAKES Annotators.
>> It will shield users initially from all of the complexities of UIMA, XML
>> Descriptors, cTAKES, etc.
>> Just check out the latest:
>> svn co http://svn.apache.org/repos/asf/ctakes/trunk
>> mvn clean compile
>> --Pei
>> [1] http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-
>> examples/src/main/java/org/apache/ctakes/examples/
>>> -----Original Message-----
>>> From: Hochheiser, Harry Stewart [mailto:harryh@pitt.edu]
>>> Sent: Thursday, June 26, 2014 5:31 PM
>>> To: Chen, Pei
>>> Subject: DeepPheno: guidance on CTakes
>>> Pei:
>>> As I'm now digging into cTAKES as part of our DeepPheno project (and
>>> some other related efforts), I'm hoping you can help with a quick
>>> question. Is there any guide/documentation on the process for adding
>>> new annotators to cTAKES?  I've dug into the apache site and mailing
>>> list archives, but haven't had much luck.
>>> Thanks!
>>> -harry
>>> ----
>>> Harry Hochheiser
>>> University of Pittsburgh
>>> Department of Biomedical Informatics
>>> harryh@pitt.edu 		412 648 9300

Harry Hochheiser
University of Pittsburgh
Department of Biomedical Informatics 
harryh@pitt.edu 		412 648 9300

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