NAME
    UMLS-Association README

  SYNOPSIS
      This package consists of Perl modules along with supporting Perl
      programs that calculate the association between CUI pairs using 
      frequency information from the Metamapped Medline baseline. 

      UMLS::Association requires the Text::NSP module to calculate the 
      association measures. Text::NSP currently implements the following 
      measures for bigrams: 

      UMLS::Association requires the UMLS::Interface module to access 
      the Unified Medical Language System (UMLS) to map input terms 
      to Concept Unique Identifiers (CUIs) and provide additional 
      information. 

      The following sections describe the organization of this software
      package and how to use it. A few typical examples are given to help
      clearly understand the usage of the modules and the supporting
      utilities.

  INSTALL
    To install the module, run the following magic commands:

      perl Makefile.PL
      make
      make test
      make install

    This will install the module in the standard location. You will, most
    probably, require root privileges to install in standard system
    directories. To install in a non-standard directory, specify a prefix
    during the 'perl Makefile.PL' stage as:

      perl Makefile.PL PREFIX=/home/programs

    It is possible to modify other parameters during installation. The
    details of these can be found in the ExtUtils::MakeMaker documentation.
    However, it is highly recommended not messing around with other
    parameters, unless you know what you're doing.

  DATABASE SETUP
    UMLS-Association assumes that the CUI bigrams extracted from the
    Metamapped Medline baseline is present as a mysql database. The names of
    these databases can be passed as configuration options at
    initialization. However, if the names of the database is not provided at
    initialization, then default values are used -- the database is called
    CUI_BIGRAMS and contains four tables: 1. N_11 2. N_1P 3. N_P1 4. N_PP

    Direction on installing the CUI_BIGRAMS database is in the INSTALL file.

    All other tables in the databases will be ignored, and any of these
    tables missing would raise an error.

    The mysql server can be on the same machine as the module or could be on
    a remotely accessible machine. The location of the server can be
    provided during initialization of the module.

  INITIALIZING THE MODULE
    To create an instance of the UMLS-Association object, using default
    values for all configuration options:

      use UMLS::Association;
      my $association = UMLS::Association->new();

    The following configuration options are also provided though:

        'driver'       -> Default value 'mysql'. This option specifies the 
                          Perl DBD driver that should be used to access the
                          database. This implies that the some other DBMS
                          system (such as PostgresSQL) could also be used,
                          as long as there exist Perl DBD drivers to
                          access the database.
        'database'     -> Default value 'CUI_BIGRAMS'. This option specifies 
                          the name UMLS-Association database. 
        'hostname'     -> Default value 'localhost'. The name or the IP 
                          address of the machine on which the database 
                          server is running.
        'socket'       -> Default value '/tmp/mysql.sock'. The socket on 
                          which the database server is using.
        'port'         -> The port number on which the database server 
                          accepts connections.
        'username'     -> Username to use to connect to the database server. 
                          If not provided, the module attempts to connect as 
                          an anonymous user.
        'password'     -> Password for access to the database server. If not
                          provided, the module attempts to access the server
                          without a password.

    These are passed through a hash. For example:

        my %options = ();
        $options{'config'}   = $config;
        $options{'database'} = 'CUI_BIGRAM_V1';

        my $association = UMLS::Association->new(\%options);

    Keep in mind that the database configuration options can be included in
    the MySQL my.cnf file. This is preferable. The directions for this are
    in the INSTALL file.

  CONTENTS
        All the modules that will be installed in the Perl system directory are
        present in the '/lib' directory tree of the package. 

        The package contains a utils/ directory that contain Perl utility 
        programs. These utilities use the modules or provide some supporting
        functionality.

          umls-association.pl         -- returns the association score of two 
                                        terms or UMLS CUIs given a specified 
                                        measure (and view of the UMLS).

         CUICollector.pl            -- script to create the CUI_BIGRAM database
                                       from the Metamapped Medline Baseline

  REFERENCING
        If you write a paper that has used UMLS-Association in some way, we'd 
        certainly be grateful if you sent us a copy.

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

        Bridget T. McInnes: btmcinnes at vcu.edu

  SOFTWARE COPYRIGHT AND LICENSE
    Copyright (C) 2015 Bridget T McInnes

    This suite of programs 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.

    Note: The text of the GNU General Public License is provided in the file
    'GPL.txt' that you should have received with this distribution.

