NAME

UMLS::Interface::CuiFinder - provides the information about CUIs in the UMLS for the modules in the UMLS::Interface package.

DESCRIPTION

This package provides the information about CUIs in the UMLS for the modules in the UMLS::Interface package.

For more information please see the UMLS::Interface.pm documentation.

SYNOPSIS

use UMLS::Interface::CuiFinder;
use UMLS::Interface::ErrorHandler;

%params = ();

$params{"realtime"} = 1;

$cuifinder = UMLS::Interface::CuiFinder->new(\%params);
die "Unable to create UMLS::Interface::CuiFinder object.\n" if(!$cuifinder);

$root = $cuifinder->_root();
print "The root is: $root\n";

$version = $cuifinder->_version();
print "The UMLS version is: $version\n";

$concept = "C0018563"; $rel = "SIB";
@array = $cuifinder->_getRelated($concept, $rel);
print "The sibling(s) of $concept is:\n";
foreach my $s (@array) { print "  => $s\n"; }
print "\n";

@array = $cuifinder->_getTermList($concept);
@array = $cuifinder->_getDefTermList($concept);
@array = $cuifinder->_getAllTerms($concept);
print "The terms of $concept are: @array\n";

$term = shift @array;
@array = $cuifinder->_getConceptList($term);
@array = $cuifinder->_getDefConceptList($term);
@array = $cuifinder ->_getAllConcepts($term);
print "The possible CUIs of the $term are: @array\n";

$hash = $cuifinder->_getCuiList();

$sab = "MSH";
$array = $cuifinder->_getCuisFromSource($sab);

@array = $cuifinder->_getSab($concept);
print "$concept exists in the following sources:\n";
foreach my $sab (@array) {  print "  => $sab\n"; }
print "\n";

@array = $cuifinder->_getChildren($concept);
print "Children of $concept @array\n";

@array = $cuifinder->_getParents($concept);
print "Parents of $concept: @array\n\n";

@array = $cuifinder->_getRelations($concept);
print "The relations of $concept: @array\n";

$concept1 = "C0018563"; $concept2 = "C0037303";

@array = $cuifinder->_getRelationsBetweenCuis($concept1, $concept2);
print "Relation(s) between $concept1 and $concept2: @array\n\n";

@array = $cuifinder->_getSt($concept);
print "The semantic type of $concept: @array\n";

$abr = "bpoc";
$string = $cuifinder->_getStString($abr);

$tui = "T12";
$string = $cuifinder->_getStAbr($tui);

$definition = $cuifinder->_getStDef($abr);
print "Definition of semantic type ($abr): $definition\n\n";


@array = $cuifinder->_getCuiDef($concept, $sabflag);
print "Definition of $concept: \n";
foreach my $el (@array) {
   print "  =>$el\n";
} 
print "\n";

my $concept = "C0376209";
$array = $cuifinder->_getExtendedDefinition($concept);
print "Extended definition of $concept: \n";
foreach my $el (@{$array}) {
   print "  => $el\n";
} 
print "\n";

$bool = $cuifinder->_exists($concept);

$hash = $cuifinder->_returnTableNames();
print "The tables currently in the index are: \n";
foreach my $t (sort keys %{$hash}) { print "  => $t\n"; }

INSTALL

To install the module, run the following magic commands:

perl Makefile.PL
make
make test
make install

This will install the module in the standard location. You will, most probably, require root privileges to install in standard system directories. To install in a non-standard directory, specify a prefix during the 'perl Makefile.PL' stage as:

perl Makefile.PL PREFIX=/home/sid

It is possible to modify other parameters during installation. The details of these can be found in the ExtUtils::MakeMaker documentation. However, it is highly recommended not messing around with other parameters, unless you know what you're doing.

SEE ALSO

http://tech.groups.yahoo.com/group/umls-similarity/

http://search.cpan.org/dist/UMLS-Similarity/

AUTHOR

Bridget T McInnes <bthomson@cs.umn.edu>
Ted Pedersen <tpederse@d.umn.edu>

COPYRIGHT

Copyright (c) 2007-2011
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 at cs.utah.edu

Serguei Pakhomov, University of Minnesota Twin Cities
pakh0002 at umn.edu

Ying Liu, University of Minnesota Twin Cities
liux0395 at 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.