This file describes how to prepare OpenNLP chunker training data from the GENIA treebank data.  

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Step 0 - prepare Genia Treebank data
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Before you can execute the steps below, you must first prepare the Genia treebank data as described in data/treebank/genia/README
You must also obtain the chunklink script as described in scripts/perl/README

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Step 1 - run chunklink_2-2-2000_for_conll.pl
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Run the chunklink script to convert Genia data to chunk data.  Please see scripts/perl/README for information on obtaining the chunklink script.

I can only get this script to work correctly using cygwin.  So, open a cygwin session and cd to data/treebank/genia to run the script.  
I have not run this script under mac or linux - but I assume that it should work fine on these platforms.  

>cd data/treebank/genia
>perl ../../../scripts/perl/chunklink_2-2-2000_for_conll.pl -NHhftc ??/wsj_????.mrg > ../../chunk/genia/genia.chunklink.chunks


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Step 2 - convert chunklink data to OpenNLP data
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The output of chunklink needs to be converted to OpenNLP format.  This can be done using the script scripts/java/data/chunk/Chunklink2OpenNLP.java:

java data.chunk.Chunklink2OpenNLP data/chunk/genia/genia.chunklink.chunks data/chunk/genia/genia.opennlp.chunks