UMLS::SenseRelate
 SYNOPSIS
   This package consists of a set of Perl modules along with supporting
   Perl programs that perform the task of Word Sense Disambiguation. The
   program(s) attempt to disambiguate the sense of a single target word in
   a given context using measures of similarity and relatedness provided by
   the UMLS::Similarity CPAN module.

 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

 CONTENTS
          lib/

            Location of the UMLS::SenseRelate::TargetWord perl module.
            Location of the UMLS::SenseRelate::AllWords perl module.

          t/

            Location of the test programs

          samples/

             A directory of scripts that demonstrate SenseClusters' usage and
             functionality.

          External/

             Contains a modified version of SemEval 2010 All Words Disambigation
             scorering program , and a script that can be run to automatically
             install it. This is used by the umls-senserelate-evaluation.pl
             program

          utils/

             Directory containing Perl utility programs. These utilities use
             the UMLS::SenseRelate modules and provide some supporting
             functionality.

 MEASURES
   UMLS-SenseRelate disambiguates terms in running text using the measures
   implemented in the UMLS-Similarity packages. Currently the following
   measures are available:

       lch    - Leacock & Chodorow (1998)
       wup    - Wu & Palmer (1994)
       nam    - Nguyen and Al-Mubaid  (2006)
       zhong  - Zhong, et al. 2002
       cdist  - Rada, et. al. 1989
       jcn    - Jiang & Conrath (1997)
       res    - Resnik (1995)
       lin    - Lin (1998)
       lesk   - Banerjee and Pedersen(2002)
       vector - Patwardhan and Pedersen (2006)
       path   - a simple path  based measure.

 CONFIGURATION FILE
   UMLS-SenseRelate passes the UMLS-Similarity package a configuration file
   which allows a specified set of sources and relations to be used when
   calculating the similarity score between two CUIs.

   There are six configuration options: SAB, REL, RELA, SABDEF, RELDEF, and
   RELADEF.

   The SAB and REL options are used to determine which sources and
   relations the path information is to be obtained from. The RELA option
   narrows down the relation even further. The RELA will only be applied to
   the PAR/CHD and RB/RN relations.

   The SABDEF and RELDEF options are used to determine which sources and
   relations to use when creating the Extended Definition. The RELA option
   narrows down the relation even further. The RELADEF will only be applied
   to the PAR/CHD and RB/RN relations.

   The path, wup, lch, lin, jcn and res measures require the SAB and REL
   options to be set. There is also an optional RELA option.

   The vector and lesk measures require the SABDEF and RELDEF options to be
   set with an optional RELADEF.

   You can specify a single source, multiple sources or the entire UMLS
   (using the UMLS_ALL option). Keep in mind that the greater the number of
   sources the larger the search space so if you obtaining path information
   about two concepts this will take longer. The names of the sources in
   the configuration file are expected to be in the SAB (source
   abbreviation) form. A listing of the sources and their SABs can be
   found:

   <http://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/re
   lease/source_vocabularies.html>

   You can specify any relations that exist in the specified set of sources
   that you defined. The directional (hierarchical) relations though are
   PAR/CHD and RB/RN. The other relations (such as RO and SIB) are not
   directional which means when obtaining path information when using these
   relations may take much longer than obtaining path information using the
   directional relations. A listing of the different relations can be found
   here (scroll down to the REL table):

   <http://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/re
   lease/abbreviations.html>

   If you do plan on using a multiple sources or the entire UMLS, we would
   advise you to use the --realtime option which is explained below, in the
   Interface.pm documentation and the path programs in the utils/
   directory. We also have a am UMLS_ALL option for this so you do not have
   to specify each and every source and relation.

   The format of the configuration file is as follows:

   SAB :: <include|exclude> <source1, source2, ... sourceN>

   REL :: <include|exclude> <relation1, relation2, ... relationN>

   RELA :: <include|exclude> <rela1, rela2, ... relaN>

   For example, if we wanted to use the MSH vocabulary with only the RB/RN
   relations, the configuration file would be:

    SAB :: include MSH
    REL :: include RB, RN

   or

    SAB :: include MSH
    REL :: exclude PAR, CHD

   If we wanted to use the SNOMEDCT vocabulary with only the PAR/CHD
   relations that are is-a relations, the configuration file would be:

    SAB :: include SNOMEDCT
    REL :: include PAR, CHD
    RELA :: include isa, inverse_isa

   The format for SABDEF and RELDEF is similar.

   The SABDEF and RELDEF options are used to determine the sources and
   relations the extended definition is to be obtained from.

   The format of the configuration file is as follows:

   SABDEF :: <include|exclude> <source1, source2, ... sourceN>

   RELDEF :: <include|exclude> <relation1, relation2, ... relationN>

   RELADEF :: <include|exclude> <rela1, rela2, ... relaN>

   Note: RELDEF takes any of MRREL relations and two special 'relations':

         1. CUI which refers to the CUIs definition

         2. TERM which refers to the terms associated with the CUI

   For example, if we wanted to use the definitions from MSH vocabulary and
   we only wanted the definition of the CUI and the definitions of the CUIs
   SIB relation, the configuration file would be:

    SABDEF :: include MSH
    RELDEF :: include CUI, SIB

   If you wanted only the PAR/CHD definitions which are is-a relations.

    SABDEF :: include MSH
    RELDEF :: include PAR, CHD
    RELADEF :: include isa, inverse_isa

   For all of these options, there is an UMLS_ALL tag. If used with SAB or
   SABDEF, it would include all of the UMLS sources. If used with the REL
   or RELDEF, it would include all of the possible relations (as well as
   CUI and TERM for RELDEF). If used with the RELA or RELADEF, it would
   include all of the RELA relations including those with no RELA relation.
   Note that this is also the default for this option which is why it is
   optional. An example of using the UMLS_ALL option is as follows:

    SAB :: include UMLS_ALL
    REL :: include UMLS_ALL

   and another is:

    SABDEF :: include UMLS_ALL
    RELDEF :: include UMLS_ALL

   If you go to the configuration file directory, there will be example
   configuration files for the different runs that you have performed.

   For more information about the configuration options please see the
   README.

 SOFTWARE COPYRIGHT AND LICENSE
   Copyright (C) 2010-2013 Bridget T McInnes, Ying Liu, Serguei Pakhomov
   and Ted Pedersen

   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.

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

   [email protected]

   You can join this group by going to:

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

   You may also contact us directly if you prefer :

     Bridget T. McInnes: bthomson at umn.edu
     Ted Pedersen      : tpederse at d.umn.edu

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

    Ted Pedersen, University of Minnesota Duluth
    tpederse at d.umn.edu

    Ying Liu, University of Minnesota
    liux0395 at umn.edu

    Serguei Pakhomov, University of Minnesota Twin Cities
    pakh002 at umn.edu

 DOCUMENTATION COPYRIGHT AND LICENSE
   Copyright (C) 2010-2012 Bridget T. McInnes, Ying Liu, Serguei Pakhomov
   and Ted Pedersen.

   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.

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