NAME
getAssociatedTerms.pl - This program returns all associated terms of a concept.
SYNOPSIS
This program takes in a CUI and returns all of its associated terms either given the sources and relations specified in the config file or in the entire UMLS.
USAGE
Usage: getAssociatedTerms.pl [OPTIONS] CUI
INPUT
Required Arguments:
CUI
Concept Unique Identifier (CUI) from the Unified Medical Language System (UMLS)
Optional Arguments:
--infile FILE
FILE is the name of a file containing a list of CUIs. The expected format is one CUI per line for example:
C0036319
C0036330
C0015230
C1533692
C0014792--config FILE
This is the configuration file. 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> (optional)
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 RELA :: include inverse_isa, isa
or
SAB :: include MSH REL :: exclude PAR, CHD
If you go to the configuration file directory, there will be example configuration files for the different runs that you have performed.
--preferred
Return only the preferred term of the CUI. When used with --config option the preferred term must be in the sources specified in the configuration file otherwise it will not return anything. Without the --config option the preferred term will be returned.
To be clear, here are the options:
1. --config FILE returns the cuis associated terms from the sources specified in the configuration file
2. --preferred --config FILE returns the cuis preferred term from the sources specified in the configuration file
3. --preferred returns the cuis preferred term
4. no config and no preferred option returns the cuis associated terms from the entire UMLS
--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.