NAME
    UMLS::Association Installation Guide

TESTING PLATFORMS
    UMLS::Association has been developed and tested on Linux primarily using
    Perl and MySQL.

SYNOPSIS
     perl Makefile.PL

     make

     make test

     make install
 
     perl CUICollector.pl --directory metamapped-baseline/2014/

DESCRIPTION
    The UMLS::Association module provides a framework for exploring the
    semantic association of terms in the Unified Medical Language System
    (UMLS).

REQUIREMENTS
  Programming Languages
     Perl (version 5.8.0 or better)

  CPAN Modules
     Text::NSP
     Compress::Zlib

  Data
    MetaMapped Medline Baseline available at
    <http://ii.nlm.nih.gov/MMBaseline>

INSTALLATION STAGES
    The installation is broken into three stages:
    Stage 1: Install Programming Languages
                  If already installed you need at minimum: 
                      - Perl version 5.10 or better

    Stage 2: Install CPAN Modules
    Stage 3: Build the bigram score database

Stage 1: Install Programming Languages, if already installed go to Stage 2
  Perl (version 5.8.5 or better)
    Perl is freely available at <http://www.perl.org>. It is very likely
    that you will already have Perl installed if you are using a Unix/Linux
    based system.

Stage 2 - Install CPAN modules, if already installed go to Stage 3
  Text::NSP
    UMLS-Association uses this package to obtain the frequency counts for
    propagation. This package is freely available at:

    <http://search.cpan.org/dist/Text-NSP/>

  Compress::Zlib
    This package is needed to read the compressed MMB output files into the
    bigram database. These files are rather large so decompressing them on
    the fly saves a tremoundous amount of space.

    The package is freely available at:
    <http://search.cpan.org/dist/Compress-Zlib/>

BUILD BIGRAM DATABASE
    Here we will process MetaMap Machine Output (MMO) formatted files into a
    database containing bigram scores for Content Unique Identifies (CUIs).
    These files are presumed to be compressed as GNU Zip archives (*.gz).

    To process a directory containing only MMO files using default database
    settings:

        CUICollector.pl --directory metamapped-baseline/2015/

    These same defaults:

        CUICollector.pl --database CUI_Bigrams --hostname localhost --port 3306 --username user --password pass --file_step 5 --directory metamapped-baseline/2015/ --verbose

    To process a single file:

        CUICollector.pl --database filename_Bigrams --files filename.txt.gz

    For a full listing of options,

        CUICollector.pl --help

    Or consult the documentation for CUICollector:

        man CUICollector.pl

CONTACT US
     If you have any trouble installing and using MMB-Interface, please 
     contact us via the users mailing list : 

     umls-association@yahoogroups.com

     You can join this group by going to:

    <http://tech.groups.yahoo.com/group/umls-association/>

     You may also contact us directly if you prefer :

     Sam Henry: henryst at vcu.edu
     Bridget T. McInnes: btmcinnes at vcu.edu

