NAME
umlsCycles.pl - This program marks problematic relations defined by the user.
SYNOPSIS
This is a utility that takes as input a list of problematic relations in the MRREL file. The relations cause cycles in structure. This programs marks the problematic relations in the MRREL file by inserting a '1' into the CVF column. It does not physicall remove a relation from the table only tags it. The bad-relations.txt file is found in the default_options directory. This file is used as the default unless one is specified on the command line.
Documentation on how the badrelation files was compiled, please refer to:
Bodenreider O. An object-oriented model for representing
semantic locality in the UMLS. Medinfo 2001;10(Pt 1):161-5.
http://mor.nlm.nih.gov/pubs/pdf/2001-medinfo-ob.pdf USAGE
Usage: umlsCycles.pl --username STRING --password STRING [OPTIONS]
INPUT
Optional Arguments:
--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
--file
File containing the bad relations. The assumption is that you are running umlsCycles from the utils directory.
DEFAULT: ../default_options/2008AA-badpairs
--unmark
It removes the marks of the the problematic relations in the MRREL file by inserting a NULL into the CVF column.
--help
Displays the quick summary of program options.
--version
Displays the version information.
OUTPUT
disambiguate.pl creates two directories. One containing the arff files and the other containing the weka files. In the weka directory, the overall averages are stored in the OverallAverage file.
SYSTEM REQUIREMENTS
Perl (version 5.8.5 or better) - http://www.perl.org
AUTHOR
Bridget T. McInnes, University of MinnesotaCOPYRIGHT
Copyright (c) 200 - 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.