NAME
findDFS.pl - This program runs a dfs over a specified set of sources and relations in the UMLS.
SYNOPSIS
This is a utility runs a dfs over a specified set of sources and relations in the UMLS returning the depth, number of paths to the root, branching factor, leaf and node count.
USAGE
Usage: findDFS.pl CONFIGFILE [OPTIONS]
INPUT
Required Arguments:
CONFIGFILE
Configuration file containing the set of sources and relations to use. The default uses MSH and the PAR/CHD relations.
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)
The SAB, REL and RELA 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 RELA :: include isa, inverse_isa
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.
Optional Arguments:
--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
--debugpath FILE
This option prints out the path information for debugging purposes.
--depth NUMBER
Searches up to the specified depth. The default is to search the complete hierarchy
--root CUI
Starts the search at a specified CUI. The default starts the search at the UMLS root node
--level NUMBER
Returns the number of CUIs above and below this NUMBER
--help
Displays the quick summary of program options.
--version
Displays the version information.
OUTPUT
The program returns the following:
1. the maximum depth
2. paths to root
3. sources
4. maximum branching factor
5. average branching factor
6. number of leaf nodes
7. number of nodes
8. rootSYSTEM 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.