Bridget McInnes > UMLS-Interface-1.33 > findDFS.pl

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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. root

SYSTEM REQUIREMENTS ^

AUTHOR ^

 Bridget T. McInnes, University of Minnesota

COPYRIGHT ^

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.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.
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