Bridget McInnes > UMLS-Interface > findCuiDepth.pl

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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 ^

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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