Bridget McInnes > UMLS-Interface-1.41 > findShortestPath.pl

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NAME ^

findShortestPath.pl - This program finds the shoretest path between two concepts.

SYNOPSIS ^

This program takes two terms or CUIs and returns the shortest path between them.

USAGE ^

Usage: findShortestPath.pl [OPTIONS] [CUI1|TERM1] [CUI2|TERM2]

INPUT ^

Required Arguments:

[CUI1|TERM1|ST1] [CUI2|TERM2|ST2]

A TERM or CUI (or some combination), or two semantic types (with the --st option) from the Unified Medical Language System

Optional Arguments:

--st

The input is two seamntic types and the shortest path between them comes from the semantic network. This can either be a TUI or the Abbreviation of the semantic type.

--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 inverse_isa, 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.

--undirected

The path between the concepts is not required to be directed such that an LCS can be obtained. This means that we can obtain a path from CUI1 to CUI2 by meandering through the graph rather than finding the CUI that subsumes both of them and then finding the shortest path between those points.

--info

This prints out the relation and source information between the CUIs in the path

--icpropagation FILE

Takes in a propagation file and then outputs the information content of the CUIs in the shortest path

--length

Prints out the length of the shortest path for ease of counting

--infile FILE

   A file containing pairs of concepts or terms in the following format:

    term1<>term2 
    
    or 

    cui1<>cui2
 
    or 
    
    cui1<>term2

    or 

    term1<>cui2

--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

--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.

--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.

--verbose

This option will print out the table information to the config directory that you specified.

--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 path(s) between the two given CUIs or terms

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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