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.

  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();

  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).

         umls-association-runDataSet.pl -- outputs the association scores of
                                           an entire dataset (such as minimayo
                                           UMNSRS, etc.)

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

        The package also contains a Apache Hadoop MapReduce java implementation
        of CUICollector.pl named CUICollectorMapReduce in the '/Hadoop' directory.
        Refer to the README file in the '/Hadoop' directory for installation and
        running instructions.

  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 :

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

  SOFTWARE COPYRIGHT AND LICENSE
    Copyright (C) 2018 Sam Henry

    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.

