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)
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) 2010-2011 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 :
umls-similarity@yahoogroups.com
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) 2010-2011 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.