NAME

nlm2mm.pl

SYNOPSIS

Converts the NLM-WSD data set to the xml-like .mm format used by the CuiTools package using current UMLS information.

DESCRIPTION

This program takes as input the National Library of Medicine's Word Sense Disambiguation (NLM-WSD) data set and converts it to our xml-like mm format for processing with the CuiTools word sense disambiguation programs.

USAGE

perl nlm2mm.pl DESTINATION Basic_Reviewed_Results DIRECTORY

The MetaMap COMMAND

    The MetaMap command used in the program is:
    $ENV{METAMAP_PATH}/metamap08 -q InputFile OutputFile
   
         where --q option outputs the data in machine code

Note: the METAMAP_PATH environment variable must be set to the bin directory containing the metamap program

    For example:
      in bash: export METAMAP_PATH=/home/bthomson/metamap/public_mm/bin
      in cshrc: set env METAMAP_PATH /home/bthomson/metamap/public_mm/bin
    
=head1 INPUT

Required Arguments:

DESTINATION

The directory that the .mm output files should go. The output file names will be named <targetword>.mm

BASIC_REVIEWED_RESULTS_DIRECTORY

This is the Basic_Reviewed_Results directory from the PMID version of the NLM-WSD data set. Note, that this program only works for the PMID version of the NLM-WSD data set.

Optional Arguments:

head3 --log DIRECTORY

Directory to contain temporary and log files. DEFAULT: nlm2mm.log

--help

Displays the quick summary of program options.

--version

Displays the version information.

OUTPUT

nlm2mm.pl converts the data set to the CuiTools xml-like .mm format.

THE .mm FORMAT

See README.mm.format

PROGRAM REQUIREMENTS

AUTHOR

 Bridget T. McInnes, University of Minnesota, Twin Cities    
=head1 COPYRIGHT

Copyright (c) 2007-2008,

 Bridget T. McInnes, University of Minnesota, Twin Cities
 bthomson at cs.umn.edu
 Ted Pedersen, University of Minnesota Duluth
 tpederse at d.umn.edu

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to

 The Free Software Foundation, Inc.,
 59 Temple Place - Suite 330,
 Boston, MA  02111-1307, USA.