getAssociatedTerms.pl - This program returns all associated terms of a concept.
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: getAssociatedTerms.pl [OPTIONS] CUI
Concept Unique Identifier (CUI) from the Unified Medical Language System (UMLS)
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
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
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.
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
Sets the debug flag for testing
Username is required to access the umls database on MySql unless it was specified in the my.cnf file at installation
Password is required to access the umls database on MySql unless it was specified in the my.cnf file at installation
Hostname where mysql is located. DEFAULT: localhost
The socket your mysql is using. DEFAULT: /tmp/mysql.sock
Database contain UMLS DEFAULT: umls
Displays the quick summary of program options.
Displays the version information.
List of CUIs that are associated with the input term
Bridget T. McInnes, University of Minnesota
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 email@example.com Serguei Pakhomov, University of Minnesota Twin Cities firstname.lastname@example.org
This 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.