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From "AndyMC@apache.org (forwarding)" <mcmurry.a...@gmail.com>
Subject Re: Brat
Date Sat, 08 Feb 2014 06:38:20 GMT
BRAT: I was just looking into BRAT because of this paper 

it is interesting that clinical text and genomic text mining are beginning to blur the lines.

A few weeks ago the $1000 genome made the news, here comes the annotation challenge. 

In the next few years we'll see more gene testing labs trying to annotate whatever clinical
indications they can get from the test order. 
Its basically essential to the gene-testing business. 

On Feb 7, 2014, at 10:49 AM, William Karl Thompson <wkt@northwestern.edu> wrote:

> Hi,
> OpenNLP has some code that takes brat annotation files and creates "BratAnnotation" object
instances. I've taken the code and modified it (simplified in some ways) to generate cTAKES
annotations, using a "BratAnnotator" analysis engine that reads in brat annotation files.
I would be happy to share that code with anyone who wants to look at it and make it better!
> -Will
> ________________________________________
> From: Chen, Pei [Pei.Chen@childrens.harvard.edu]
> Sent: Friday, February 07, 2014 12:43 PM
> To: dev@ctakes.apache.org
> Subject: RE: Brat
> I think some of the OpenNLP folks did some work with the Brat annotation tool,
> but I don't think anyone has worked on it with cTAKES-I would be curious on your analysis
>> -----Original Message-----
>> From: John Green [mailto:john.travis.green@gmail.com]
>> Sent: Friday, February 07, 2014 6:01 AM
>> To: dev@ctakes.apache.org
>> Subject: Brat
>> I've done a cursory search and come up short: has anyone written anything
>> to convert the annotations from the pipeline to the Brat *.ann format?
>> Thanks,
>> JG

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