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: 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): 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 :: REL :: RELA :: 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 :: RELDEF :: RELADEF :: 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 : umls-similarity@yahoogroups.com You can join this group by going to: 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: and is included in this distribution as FDL.txt.