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
    UMLS-Interface REQUIRES that the following software packages and data:

  Programming Languages
     Perl (version 5.8.0 or better)

  CPAN Modules
     DBI
     DBD::mysql
     Text::NSP
     Compress::Zlib
 
     and of course,
     UMLS::Interface

  Database
    MySQL (version 5 or better)

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

INSTALLATION STAGES
    The installation is broken into four 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: Install MySQL
                  If already installed you need at minimum: 
                      - MySQL version 5 or better

    Stage 4: Build the bigram score database
    Stage 5: Install UMLS-Association

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
  DBI
    CPAN modules, and will not be repeated in detail for each module.****

    UMLS-Interface uses DBI to access the mysql database containing the
    UMLS. DBI is freely available at <http://search.cpan.org/~timb/DBI/>

    If you have supervisor access, or have configured MCPAN for local
    install, you can install via:

     perl -MCPAN -e shell
     > install DBI

    If not, you can, "manually" install by downloading the *.tar.gz file,
    unpacking, and executing the following commands.

     perl Makefile.PL PREFIX=/home/programs LIB=/home/lib
     make
     make test
     make install

    Note that the PREFIX and LIB settings are just examples to help you
    create a local install, if you do not have supervisor (su) access.

    You must include /home/MyPerlLib in your PERL5LIB environment variable
    to access this module when running.

  DBD::mysql
    UMLS::Association uses this module to connect, create, and add to the
    bigram score database with the MySQL database management system. It is
    the MySQL sriver for the Perl5 Database interface.

    This package is freely available at
    <http://search.cpan.org/dist/DBD-mysql/>

  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/>

  UMLS::Interface
    The core UMLS package provides a dictionary from content unqiue
    identifiers (CUI) to their meanings in the Unified Medical Language
    System. Refer to the UMLS::Interface documentation for how to install
    the UMLS database on your system.

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

Stage 3 - Install MySQL, if already installed go to Stage 4
    Requires MySQL (version 5 or better)

    MySQL is a freely available database at <http://www.mysql.com/>. You may
    be able to install this with you package manager. Otherwise you will
    have to download the appropriate files from the MySQL website. Either
    way, make certain that the following are installed:

            1. Server
            2. Client
            3. Shared libraries
            4. Headers and libraries

    Sometimes the headers and libraries are not installed so you want to
    double check on that.

  Installing on Fedora using yum
    To install mysql using yum, type the following three commands on the
    command line:

        1. yum install mysql
        2. yum install mysql-server
        3. yum install mysql-devel

    After this is complete mysql should be installed. Next you need to start
    the mysql server by typing the following command:

         service mysqld start

  Installing on Ubuntu using apt-get
    Type the following commands as root or with sudo:

     apt-get install mysql-common
     apt-get install mysql-client
     apt-get install mysql-server
 
     service mysqld start

  Reminder
    Also for all the installations, remember to set your root password:

         /usr/bin/mysqladmin -u root password 'new-password'

    If you are not going to be using root as your main entry into mysql -
    which is probably a good idea - you can create a user account. Here is
    how I did it:

     mysql> CREATE USER bthomson IDENTIFIED BY 'psswrd';
     Query OK, 0 rows affected (0.00 sec)

     mysql> GRANT ALL ON *.* TO bthomson;
     Query OK, 0 rows affected (0.00 sec)

    Directions are in the mysql documentation:

    <http://dev.mysql.com/doc/refman/5.1/en/adding-users.html>

Stage 4: Build Bigram Database
    Here we will process MetaMap Machine Output (MMO) formatted files into a
    databasecontaining bigram scores for Content Unique Identifies (CUIs).
    These files arepresumed to be compressed as GNU Zip archives (*.gz). You
    can download the MetaMap Medline Baseline from the National Library of
    Medicine:

    <http://ii.nlm.nih.gov/MMBaseline/index.shtml>

    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

Stage 5: Install UMLS-Association package
    The usual way to install the package is to run the following commands:

         perl Makefile.PL
         make
         make test
         make install

    You will often need root access/superuser privileges to run make
    install. The module can also be installed locally. To do a local
    install, you need to specify a PREFIX option when you run 'perl
    Makefile.PL'. For example,

     perl Makefile.PL PREFIX=/home

     or

     perl Makefile.PL LIB=/home/lib PREFIX=/home

    will install UMLS-Interface into /home. The first method above will
    install the modules in /home/lib/perl5/site_perl/5.8.3 (assuming you are
    using version 5.8.3 of Perl; otherwise, the directory will be slightly
    different). The second method will install the modules in /home/lib. In
    either case the executable scripts will be installed in /home/bin and
    the man pages will be installed in home/share.

    Warning: do not put a dash or hyphen in front of PREFIX, or LIB

    In your perl programs that you may write using the modules, you may need
    to add a line like so

     use lib '/home/lib/perl5/site_perl/5.8.3';

    if you used the first method or

     use lib '/home/lib';

    if you used the second method. By doing this, the installed modules are
    found by your program. To run the umls-association.pl program, you would
    need to do

     perl -I/home/lib/perl5/site_perl/5.8.3 umls-association.pl

     or

    perl -I/home/lib

    Of course, you could also add the 'use lib' line to the top of the
    program yourself, but you might not want to do that. You will need to
    replace 5.8.3 with whatever version of Perl you are using. The preceding
    instructions should be sufficient for standard and slightly non-standard
    installations. However, if you need to modify other makefile options you
    should look at the ExtUtils::MakeMaker documentation. Modifying other
    makefile options is not recommended unless you really, absolutely, and
    completely know what you're doing!

    NOTE: If one (or more) of the tests run by 'make test' fails, you will
    see a summary of the tests that failed, followed by a message of the
    form "make: *** [test_dynamic] Error Y" where Y is a number between 1
    and 255 (inclusive). If the number is less than 255, then it indicates
    how many test failed (if more than 254 tests failed, then 254 will still
    be shown). If one or more tests died, then 255 will be shown. For more
    details, see:

    <http://search.cpan.org/dist/Test-Simple/lib/Test/Builder.pm#EXIT_CODES>

CONTACT US
     If you have any trouble installing and using UMLS-Association, 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 :

     Bridget T. McInnes: btmcinnes at vcu.edu
     Keith Herbert: herbertkb at vcu.edu

