SemMed-Interface
  SYNOPSIS
      The SemMed-Interface is a suite of Perl modules that utilize path information
      present in the Semantic Medline Database in order to calculate the semantic
      association between two concepts in the UMLS.

  INSTALL
        To install these modules run:

          perl Makefile.PL
          make
          make test
          make install

        This will install the modules in the standard locations. 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

        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.

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

          SemMed/Interface.pm
              SemMed/Interface/CUI.pm
              SemMed/Interface/Predicate.pm
              SemMed/Interface/GraphTraversal.pm
              SemMed/Interface/DataAccess.pm

        -- present in the lib/ subdirectory. All these modules, once installed
        in the Perl system directory, can be directly used by Perl programs.

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

          nanob2b-example.pl         -- simple example of using the module

  CONFIGURATION
    The SemMed-Interface requires access to the Semantic Medline Database.
    Please install this database onto your MySQL server and follow the
    set-up steps found in the INSTALL file.

  SOFTWARE COPYRIGHT AND LICENSE
        Copyright (C) 2016 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.

  REFERENCING
        This is where you would add the paper referencing the packge. For 
        example: 

        If you write a paper that has used SemMed-Interface in some way, we'd 
        certainly be grateful if you sent us a copy and referenced: 

        @inproceedings{McInnesPP09,
           title={{UMLS-Interface and NanoB2B-Example : Open Source 
                   Software for Measuring Paths and Semantic Similarity}}, 
           author={McInnes, B.T. and Pedersen, T. and Pakhomov, S.V.}, 
           booktitle={Proceedings of the American Medical Informatics 
                      Association (AMIA) Symposium},
           year={2009}, 
           month={November}, 
           address={San Fransisco, CA}
        }

        This paper is also found in
        <http://www-users.cs.umn.edu/~bthomson/publications/pubs.html>
        or
        <http://www.d.umn.edu/~tpederse/Pubs/amia09.pdf>

  REFERENCES
        1   <reference 1>

        2   <reference 2> s

  SEE ALSO
    <http://search.cpan.org/dist/NanoB2B-Example>

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

    <mailing list email>

    You can join this group by going to:

    <mailing list website>

    You may also contact us directly if you prefer :

      Bridget T. McInnes: btmcinnes at vcu.edu

  AUTHORS
     Bridget T McInnes, University of Minnesota Twin Cities
     bthomson at cs.umn.edu

     Andriy Y. Mulyar

  DOCUMENTATION COPYRIGHT AND LICENSE
    Copyright (C) 2016 Bridget T. McInnes

    Permission is granted to copy, distribute and/or modify this document
    under the terms of the GNU Free Documentation License, Version 1.2 or
    any later version published by the Free Software Foundation; with no
    Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.

    Note: a copy of the GNU Free Documentation License is available on the
    web at:

    <http://www.gnu.org/copyleft/fdl.html>

    and is included in this distribution as FDL.txt.

