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 Release Date: July 9, 2005
 Matt Lease <mlease@cs.brown.edu>
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 This distribution contains data and source code supporting the work described in:

	Matthew Lease and Eugene Charniak
	Parsing Biomedical Literature
	Second International Joint Conference on Natural Language Processing (IJCNLP'05).

 Source code:

 * version of the Charniak parser which allows a distinct part-of-speech (POS) tagger training step (for
   the case of POS tags being available but no treebank)

 * tokenization has been turned off, assuming the data to be parsed
   has been pre-tokenized. It can be turned on by a trivial code
   change in parseIt.C, though the tokenizer assumes PTB conventions -- grep on "###".

 Data:

 * Brown-GENIA treebank (21 abstracts containing 215 sentences from
   GENIA). As of GENIA treebank beta2, BBT comprises a disjoint set of
   abstracts (99101510-99120900), so the two may be used in combination.

 * trained parsing parameters for WSJ + GENIA POS-training.

 ======
 Parser
 ======

 This distribution represents a branch off the Nov. 2001 version of the parser (built with g++ 2.95), 
 but it includes bug fixes to the parser through its Nov. 2003 release. Subsequent improvements/changes
 to the parser have not been integrated into this version.

 The standard parser documentation can be found in parseIt/README and TRAIN/README

 Run the parser using "parse.sh".  This simple script just unlimits the stack size (to avoid segfaults
 on complex sentences), allows sentence lengths up to 100 words, and uses 21x over-parsing.

 To train the parser, use "train.sh".

 DATA_3.02/ is the parser's data directory after training it on WSJ as usual + training its POS tagger
 on the 1,778 abstracts from GENIA not in the combined treebank (see paper for details).  

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