NAME
getExtendedDef.pl - This program returns the extended definition of a concept or a term.
SYNOPSIS
This program takes in a CUI or a term and returns its extended definition consisting of the its definition, the definition of its all of its relations.
USAGE
Usage: getExtendedDef.pl [OPTIONS] [CUI|TERM]
INPUT
Required Arguments:
[CUI|TERM}
Concept Unique Identifier (CUI) or a term from the Unified Medical Language System (UMLS)
Optional Arguments:
--config FILE
This is the configuration file. The format of the configuration file is as follows:
SABDEF :: <include|exclude> <source1, source2, ... sourceN>
RELDEF :: <include|exclude> <relation1, relation2, ... relationN>
SABDEF refers to the sources in which the definitions can come from. RELDEF refers to the relations in which the definitions can come from.
The possible relations that can be included in RELDEF are: 1. all of the possible relations in MRREL such as PAR, CHD, ... 2. CUI which refers the concepts definition 3. ST which refers to the concepts semantic types definition 4. TERM which refers to the concepts associated terms
For example, if we wanted to use the MSH vocabulary and we wanted to use the terms, the CUIs definition and the CUIs parent definition and its semantic type definition as the extended definition the configuration file would be:
SABDEF :: include MSH RELDEF :: include TERM, CUI, PAR, ST or
SABDEF :: include MSH
If you go to the configuration file directory, there will be example configuration files for the different runs that you have performed.
The default is:
SABDEF :: include UMLS_ALL RELDEF :: include UMLS_ALL
which uses all of the sources and all of the relations.
--debug
Sets the debug flag for testing
--username STRING
Username is required to access the umls database on MySql unless it was specified in the my.cnf file at installation
--password STRING
Password is required to access the umls database on MySql unless it was specified in the my.cnf file at installation
--hostname STRING
Hostname where mysql is located. DEFAULT: localhost
--socket STRING
The socket your mysql is using. DEFAULT: /tmp/mysql.sock
--database STRING
Database contain UMLS DEFAULT: umls
--help
Displays the quick summary of program options.
--version
Displays the version information.
OUTPUT
List of CUIs that are associated with the input term
SYSTEM REQUIREMENTS
Perl (version 5.8.5 or better) - http://www.perl.org
AUTHOR
Bridget T. McInnes, University of MinnesotaCOPYRIGHT
Copyright (c) 2007-2009,
Bridget T. McInnes, University of Minnesota
bthomson at cs.umn.edu
Ted Pedersen, University of Minnesota Duluth
tpederse at d.umn.edu
Siddharth Patwardhan, University of Utah, Salt Lake City
sidd@cs.utah.edu
Serguei Pakhomov, University of Minnesota Twin Cities
pakh0002@umn.eduThis program 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.