umlsCycles.pl - This program marks problematic relations defined by the user.
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: umlsCycles.pl --username STRING --password STRING [OPTIONS]
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
File containing the bad relations. The assumption is that you are running umlsCycles from the utils directory.
DEFAULT: ../default_options/2008AA-badpairs
It removes the marks of the the problematic relations in the MRREL file by inserting a NULL into the CVF column.
Displays the quick summary of program options.
Displays the version information.
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.
Bridget T. McInnes, University of Minnesota
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.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.
