ALBD

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INSTALL  view on Meta::CPAN

    UMLS::Association requires that a database can be connected to that is
    in the correct format. Although this database is not required for ALBD
    (since co-occurrence data is loaded from a co-occurrence matrix), it is
    required to run UMLS:Association. If you ran UMLS::Association to
    generate a co-occurrence matrix, you should be fine. Otherwise you will
    need to create a dummy database that it can connect to. This can be done
    in a few steps:

    1) open mysql type mysql at the terminal

    2) create the default database in the correct format, type: CREATE
    DATABASE cuicounts; use cuicounts; CREATE TABLE N_11(cui_1 CHAR(10),
    cui_2 CHAR(10), n_11 BIGINT(20));

CONTACT US
    If you have any trouble installing and using ALBD, please contact us us
    directly :

        Sam Henry: henryst at vcu.edu

        Bridget McInnes: btmcinnes at vcu.edu

README  view on Meta::CPAN

    UMLS::Association requires that a database can be connected to that is
    in the correct format. Although this database is not required for ALBD
    (since co-occurrence data is loaded from a co-occurrence matrix), it is
    required to run UMLS:Association. If you ran UMLS::Association to
    generate a co-occurrence matrix, you should be fine. Otherwise you will
    need to create a dummy database that it can connect to. This can be done
    in a few steps:

    1) open mysql type mysql at the terminal

    2) create the default database in the correct format, type: CREATE
    DATABASE cuicounts; use cuicounts; CREATE TABLE N_11(cui_1 CHAR(10),
    cui_2 CHAR(10), n_11 BIGINT(20));

  INITIALIZING THE MODULE
    To create an instance of the ALBD object, using default values for all
    configuration options: %options = (); $options{'lbdConfig'} =
    'configFile'; my $lbd = LiteratureBasedDiscovery->new(\%options);
    $lbd->performLBD();

    The following configuration options are also provided though:

    'assocConfig' path to a UMLS::Association configuration file. Default
    location is 'config/association'. Replace this file for your computer to
    avoid having to specify each time

lib/ALBD.pm  view on Meta::CPAN

# Initializes everything needed for Literature Based Discovery
# input: $optionsHashRef <- reference to LBD options hash (command line input)
# output: none, but global parameters are set
sub _initialize {
    my $self = shift;
    my $optionsHashRef = shift; 

    #initialize UMLS::Interface
    my %tHash = ();
    $tHash{'t'} = 1; #default hash values are with t=1 (silence module output)
    my $componentOptions = \%tHash;
    if (${$optionsHashRef}{'interfaceConfig'} ne '') {
	#read configuration file if its defined
	$componentOptions = 
	    $self->_readConfigFile(${$optionsHashRef}{'interfaceConfig'});
    }
    #else use default configuration
    $umls_interface = UMLS::Interface->new($componentOptions) 
	or die "Error: Unable to create UMLS::Interface object.\n";

    #initialize UMLS::Association
    $componentOptions = \%tHash;
    if (${$optionsHashRef}{'assocConfig'} ne '') {
	#read configuration file if its defined
	$componentOptions = 
	    $self->_readConfigFile(${$optionsHashRef}{'assocConfig'});
    }
    #else use default configuation
    $umls_association = UMLS::Association->new($componentOptions) or 
	die "Error: Unable to create UMLS::Association object.\n";

    #initialize LBD parameters
    %lbdOptions = %{$self->_readConfigFile(${$optionsHashRef}{'lbdConfig'})};
    
}    

# Reads the config file in as an options hash
# input: the name of a configuration file that has key fields in '<>'s, 
#        The '>' is followed directly by the value for that key, no space.
#        Each line of the file contains a new key-value pair (e.g. <key>value)
#        If no value is provided, a default value of 1 is set
# output: a hash ref to a hash containing each key value pair
sub _readConfigFile {
    my $self = shift;
    my $configFileName = shift;
    
    #read in all options from the config file
    open IN, $configFileName or die("Error: Cannot open config file: $configFileName\n");
    my %optionsHash = ();
    my $firstChar;
    while (my $line = <IN>) {

lib/ALBD.pm  view on Meta::CPAN

		print STDERR 
		    "Warning: Invalid line in $configFileName: $line\n";
	    }
	    else {
		#data was grabbed from the line, add to hash
		if ($2) {
		    #add key and value to the optionsHash
		    $optionsHash{$1} = $2;
		}
		else {
		    #add key and set default value to the optionsHash
		    $optionsHash{$1} = 1;
		}
	    }
	}
    }
    close IN;

    return \%optionsHash;
}

lib/LiteratureBasedDiscovery/Discovery.pm  view on Meta::CPAN

    #  set up database
    my $db = $cuiFinder->_getDB(); 
    
    # retreive the table as a nested hash where keys are CUI1, 
    # then CUI2, value is N11
     my @keyFields = ('cui_1', 'cui_2');
     my $matrixRef = $db->selectall_hashref(
	"select * from $tableName", \@keyFields);

    # set values of the loaded table to n_11
    # ...default is hash of hash of hash
    foreach my $key1(keys %{$matrixRef}) {
	foreach my $key2(keys %{${$matrixRef}{$key1}}) {
	    ${${$matrixRef}{$key1}}{$key2} = ${${${$matrixRef}{$key1}}{$key2}}{'n_11'};
	}
    }
    return $matrixRef;
}
=cut

1;

lib/LiteratureBasedDiscovery/Rank.pm  view on Meta::CPAN

# Builds a list of B->C term pairs that also co-occurr with A terms
# Only adds B->C term pairs for C terms that are also present in the 
# implicitMatrix.
# The value of the bcPairs Hash is the value in the explicit matrix 
# for that pair.
# input:  $startingMatrixRef <- ref to the starting matrix
#         $explicitMatrixRef <- ref to the explicit matrix
#         $implicitMatrixRef <- ref to the implicit matrix
# output: a hash ref of BC term pairs. Each key is "$bTerm,$cTerm", 
#         value is by default the frequency of BC co-occurrences in the 
#         matrix
sub _getBCPairs {
    my $startingMatrixRef = shift;
    my $explicitMatrixRef = shift;
    my $implicitMatrixRef = shift;

    #get all bTerms
    my %bTerms = ();
    my $rowRef;
    foreach my $rowKey (keys %{$startingMatrixRef}) {

utils/runDiscovery.pl  view on Meta::CPAN

."   runDiscovery lbdConfigFile\n";
;

#############################################################################
#                       Parse command line options 
#############################################################################
my $DEBUG = 0;      # Prints EVERYTHING. Use with small testing files.        
my $HELP = '';      # Prints usage and exits if true.
my $VERSION;

#set default param values
my %options = ();
$options{'assocConfig'}  = '';
$options{'interfaceConfig'} = '';

#grab all the options and set values
GetOptions( 'debug'             => \$DEBUG, 
            'help'              => \$HELP,
	    'version'           => \$VERSION,
            'assocConfig=s'     => \$options{'assocConfig'},
            'interfaceConfig=s' => \$options{'interfaceConfig'},