getCuiList.pl - This program returns a list of CUIs based on the configuration file.
This program returns a list of CUIs based on the sources and relations specified in the configuration file.
Usage: getCuiList.pl [OPTIONS] CONFIGFILE
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.
List of CUIs that are associated with the input term
Returns the number of children of a given CUI. The format for just using --children is:
CUI children
Returns the number of children of a given CUI. The format for just using --parents is:
CUI parents
The format for using both --parents and --children is:
CUI children|parents
Returns the number of relations of a given CUI. The REL input can be a list of comma seperated relations. For example:
--relation "SIB,RO"
This would return the number of SIB and RO relations for a given concept in the format : CUI sib|ro
This option current can not be used with the --children and --parent option because if you want them just add them to the list. For example: --relation "SIB,PAR,CHD"
Returns the terms associated with the CUI in the following format:
CUI term1|term2|term3|...
If used with the --parents and/or --children options or the --relation options, the following format is returned:
CUI children|parents|term1|term2|...
Remember children and parents is a number!
Returns only those CUIs with the specified semantic type
Returns only those CUIs with the specified semantic group
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.
Perl (version 5.8.5 or better) - http://www.perl.org
Bridget T. McInnes, University of Minnesota
Copyright (c) 2007-2011,
Bridget T. McInnes, University of Minnesota bthomson at cs.umn.edu Ted Pedersen, University of Minnesota Duluth tpederse at d.umn.edu Serguei Pakhomov, University of Minnesota Twin Cities pakh0002@umn.edu
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.
To install UMLS::Interface, copy and paste the appropriate command in to your terminal.
cpanm
cpanm UMLS::Interface
CPAN shell
perl -MCPAN -e shell install UMLS::Interface
For more information on module installation, please visit the detailed CPAN module installation guide.