NAME
findCuiDepth.pl - This program returns the minimum and maximum depth of a given CUI or term.
SYNOPSIS
This program takes in a CUI or a term and returns its minimum and maximum depth.
USAGE
Usage: findCuiDepth.pl [OPTIONS] [TERM|CUI]
INPUT
Required Arguments:
[TERM|CUI]
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:
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 isa, inverse_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.
--debug
This sets the debug flag for testing
--infile FILE
This option takes a list of CUIs or TERMs and returns their depth. Note one CUI or TERM per line is the expected format.
--minimum
Finds just the minimum CUI depth
--maximum
Finds just the maximum CUI depth
--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
--realtime
This option will not create a database of the path information for all of concepts in the specified set of sources and relations in the config file but obtain the information for just the input concept
--forcerun
This option will bypass any command prompts such as asking if you would like to continue with the index creation.
--verbose
This option will print out the table information to the config file that you specified.
--debugpath FILE
This option prints out the path information for debugging purposes. This option is only really available with the --reatime option because otherwise the path information is stored in the database. You can get this information in a file if you use the --verbose option while creating the index.
--cuilist FILE
This option takes in a file containing a list of CUIs (one CUI per line) and stores only the path information for those CUIs rather than for all of the CUIs given the specified set of sources and relations
--help
Displays the quick summary of program options.
--version
Displays the version information.
OUTPUT
The minimum depth of a given CUI or term
CONFIGURATION FILE
There exist a configuration files to specify which source and what relations are to be used. The default source is the Medical Subject Heading (MSH) vocabulary and the default relations are the PAR/CHD relation.
The format of the configuration file is as follows:
SAB :: <include|exclude> <source1, source2, ... sourceN>
REL :: <include|exclude> <relation1, relation2, ... relationN>
The SAB and REL are for specifing what sources and relations should be used when traversing the UMLS. 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 if we wanted to use MSH and use any relation except for PAR/CHD, the configuration would be:
SAB :: include MSH REL :: exclude PAR, CHD
An example of the configuration file can be seen in the samples/ directory.
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.