File Coverage

blib/lib/WWW/Search/PharmGKB.pm

Criterion	Covered	Total	%
statement	1	3	33.3
branch			n/a
condition			n/a
subroutine	1	1	100.0
pod			n/a
total	2	4	50.0

package WWW::Search::PharmGKB;

use SOAP::Lite;
import SOAP::Data 'type';
use English;
use Carp;
use vars qw($VERSION);
use Data::Dumper;

$VERSION = '2.01';

sub new {
    my $class = shift;
    my $self = bless {
        proxy => 'http://www.pharmgkb.org/services/PharmGKBItem',
        uri => 'PharmGKBItem',
        readable => 1,
    },
    $class;
    return $self;
}

sub gene_search {

    my $self = shift;
    my($gene) = @_;
    my $result_obj = {};
    my $pharm_ids = $self->_search($gene, 'Gene');
    if($pharm_ids) {

        foreach my $gene_id(@{$pharm_ids}) {
            my $local_hash = {};
            my $soap_service = SOAP::Lite
		-> readable ($self->{readable})
		-> uri($self->{uri})
		-> proxy($self->{proxy})
		-> searchGene ($gene_id);
	    my $search_result = $soap_service->result;
	    $local_hash->{'alternate_names'} = '';
	    $local_hash->{'drugs'} = '';
	    $local_hash->{'diseases'} = '';
	    $local_hash->{'phenotypes'} = '';
	    $local_hash->{'pathways'} = '';
	    $local_hash->{'alternate_symbols'} = '';
	    $local_hash->{'name'} = '';
	    $local_hash->{symbol} = '';

            my @pathways = ();
	    if($search_result->{'geneRelatedPathways'}) {
		my $pathway_result = $search_result->{'geneRelatedPathways'};

		for(my $i = 0; $i
		    push(@pathways, {$pathway_result->[$i] => $pathway_result->[$i+1]});
		}
	    }
            $local_hash->{'pathways'} = \@pathways;
	    if($search_result->{geneName}) {
		$local_hash->{name} = $search_result->{geneName};
	    }
	    if($search_result->{geneSymbol}) {
		$local_hash->{symbol} = $search_result->{geneSymbol};
	    }
            if($search_result->{'geneAlternateNames'}) {
		$local_hash->{'alternate_names'} = $search_result->{'geneAlternateNames'};
	    }
	    if($search_result->{'geneRelatedDrugs'}) {
		$local_hash->{'drugs'} = $search_result->{'geneRelatedDrugs'};
	    }
	    if($search_result->{'geneRelatedDiseases'}) {
		$local_hash->{'diseases'} = $search_result->{'geneRelatedDiseases'};
	    }
	    if($search_result->{'geneAlternateSymbols'}) {
		$local_hash->{'alternate_symbols'} = $search_result->{'geneAlternateSymbols'};
	    }
	    if($search_result->{'geneRelatedPhenotypeDatasets'}) {
		$local_hash->{'phenotypes'} = $search_result->{'geneRelatedPhenotypeDatasets'};
	    }

            $result_obj->{$gene_id} = $local_hash;
        }
    }
    else {
        print "Gene $gene was not found in PharmGKB!\n";
    }
    return $result_obj;
}

sub disease_search {

    my $self = shift;
    my($disease) = @_;
    my $result_obj = {};
    my $pharm_ids;
    if($disease) {
        $pharm_ids = $self->_search($disease, 'Disease');
    }
    else {
        print "\'$disease\' is weird. I can't search that\n";
        return 0;
    }

    if($pharm_ids) {

        foreach my $disease_id(@{$pharm_ids}) {
            my $local_hash = {};
            my $soap_service = SOAP::Lite
		-> readable (1)
		-> uri($self->{uri})
		-> proxy($self->{proxy})
		-> searchDisease ($disease_id);


	    my $search_result = $soap_service->result;
	    $local_hash->{'names'} = '';
	    $local_hash->{'drugs'} = '';
	    $local_hash->{'genes'} = '';
	    $local_hash->{'phenotypes'} = '';
	    $local_hash->{'pathways'} = '';

	    my @pathways = ();
	    if($search_result->{'diseaseRelatedPathways'}) {
		my $pathway_result = $search_result->{'diseaseRelatedPathways'};

		for(my $i = 0; $i
		    push(@pathways, {$pathway_result->[$i] => $pathway_result->[$i+1]});
		}
	    }
            $local_hash->{'pathways'} = \@pathways;
	    if($search_result->{'diseaseAlternateNames'}) {
		$local_hash->{'names'} = $search_result->{'diseaseAlternateNames'};
	    }
	    if($search_result->{'diseaseRelatedDrugs'}) {
		$local_hash->{'drugs'} = $search_result->{'diseaseRelatedDrugs'};
	    }
	    if($search_result->{'diseaseRelatedGenes'}) {
		$local_hash->{'genes'} = $search_result->{'diseaseRelatedGenes'};
	    }
	    if($search_result->{'diseaseRelatedPhenotypeDatasets'}) {
		$local_hash->{'phenotypes'} = $search_result->{'diseaseRelatedPhenotypeDatasets'};
	    }

            $result_obj->{$disease_id} = $local_hash;
        }
    }
    else {
        print "Disease $disease was not found in PharmGKB!\n";
    }
    return $result_obj;
}

sub drug_search {
    my $self = shift;
    my($drug) = @_;
    my $result_obj = {};
    my $pharm_ids;
    if($drug) {
        $pharm_ids = $self->_search($drug, 'Drug');
    }
    else {
        print "\'$drug\' is weird. I can't search that\n";
        return 0;
    }
    if($pharm_ids) {
        foreach my $drug_id(@{$pharm_ids}) {
            my $local_hash = {};
            my $soap_service = SOAP::Lite
		-> readable (1)
		-> uri($self->{uri})
		-> proxy($self->{proxy})
		-> searchDrug ($drug_id);

	    my $search_result = $soap_service->result;
	    $local_hash->{'generic_names'} = '';
	    $local_hash->{'trade_names'} = '';
	    $local_hash->{'category'} = '';
	    $local_hash->{'classification'} = '';
	    $local_hash->{'genes'} = '';
	    $local_hash->{'diseases'} = '';
	    $local_hash->{'phenotypes'} = '';
	    $local_hash->{'pathways'} = '';
	    $local_hash->{'name'} = '';
            my @pathways = ();
	    if($search_result->{'drugRelatedPathways'}) {
		my $pathway_result = $search_result->{'drugRelatedPathways'};

		for(my $i = 0; $i < scalar(@{$pathway_result}); $i+= 2) {
		    push(@pathways, {$pathway_result->[$i] => $pathway_result->[$i+1]});
		}
	    }
            $local_hash->{'pathways'} = \@pathways;
	    if($search_result->{'drugName'}) {
		$local_hash->{'name'} = $search_result->{'drugName'};
	    }
	    if($search_result->{'drugGenericNames'}) {
		$local_hash->{'generic_names'} = $search_result->{'drugGenericNames'};
	    }
	    if($search_result->{'drugTradeNames'}) {
		$local_hash->{'trade_names'} = $search_result->{'drugTradeNames'};
	    }
	    if($search_result->{'drugCategory'}) {
		$local_hash->{'category'} = $search_result->{'drugCategory'};
	    }
	    if($search_result->{'drugVaClassifications'}){
		$local_hash->{'classification'} = $search_result->{'drugVaClassifications'};
	    }
	    if($search_result->{'drugRelatedGenes'}) {
		$local_hash->{'genes'} = $search_result->{'drugRelatedGenes'};
	    }
	    if($search_result->{'drugRelatedDiseases'}) {
		$local_hash->{'diseases'} = $search_result->{'drugRelatedDiseases'};
	    }
	    if($search_result->{'drugRelatedPhenotypeDatasets'}) {
		$local_hash->{'phenotypes'} = $search_result->{'drugRelatedPhenotypeDatasets'};
	    }

            $result_obj->{$drug_id} = $local_hash;
        }
    }
    else {
        print "Drug $drug was not found in PharmGKB!\n";
    }
    return $result_obj;
}

sub publication_search {

    my $self = shift;
    my($search_term) = @_;
    my $pharm_ids;
    my $result_obj = {};
    if($search_term) {
	$pharm_ids = $self->_search($search_term, 'Publication');
    }
    else {
	print "\'$search_term\' is weird. I can't search that\n";
	return 0;
    }
    if($pharm_ids) {
	foreach my $id(@{$pharm_ids}) {
	    my $local_hash = {};
	    my $soap_service = SOAP::Lite
		-> readable ($self->{readable})
		-> uri($self->{uri})
		-> proxy($self->{proxy})
		-> searchPublication ($id);

	    my $search_result = $soap_service->result;
	    $local_hash->{'grant_id'} = '';
	    $local_hash->{'journal'} = '';
	    $local_hash->{'title'} = '';
	    $local_hash->{'month'} = '';
	    $local_hash->{'abstract'} = '';
	    $local_hash->{'authors'} = '';
	    $local_hash->{'volume'} = '';
	    $local_hash->{'page'} = '';
	    $local_hash->{'cross_reference'} = '';
	    $local_hash->{'year'} = '';
	    if($search_result) {
		if($search_result->{publicationGrantIds}) {
		    $local_hash->{'grants_id'} = $search_result->{publicationGrantIds};
		}
		if($search_result->{publicationJournal}) {
		    $local_hash->{journal} = $search_result->{publicationJournal};
		}
		if($search_result->{publicationName}) {
		    $local_hash->{title} = $search_result->{publicationName};
		}
		if($search_result->{publicationMonth}) {
		    $local_hash->{month} = $search_result->{publicationMonth};
		}
		if($search_result->{publicationAbstract}) {
		    $local_hash->{'abstract'} = $search_result->{publicationAbstract};
		}
		if($search_result->{publicationAuthors}) {
		    $local_hash->{authors} = $search_result->{publicationAuthors};
		}
		if($search_result->{publicationVolume}) {
		    $local_hash->{volume} = $search_result->{publicationVolume};
		}
		if($search_result->{publicationPage}) {
		    $local_hash->{page} = $search_result->{publicationPage};
		}
		if($search_result->{publicationAnnotationCrossReference}) {
		    my $references = $search_result->{publicationAnnotationCrossReference};
		    my @references_array = ();
		    for(my $i=0; $i < scalar(@{$references});$i+=2) {
			push(@references_array, {$references->[$i] => $references->[$i+1]});
		    }
		    $local_hash->{'cross_reference'} = \@references_array;
		}
		if($search_result->{publicationYear}) {
		    $local_hash->{year} = $search_result->{publicationYear};
		}
	    }
	    $result_obj->{$id} = $local_hash;
	}
    }
    else {
	print "No results found for $search_term\n";
    }
    return $result_obj;
}


sub _search {
    my $self = shift;
    my($search_term, $key) = @_;
    my @pharm_id = ();

    my $soap_service = SOAP::Lite
        -> readable ($self->{readable})
	-> uri('SearchService')
	-> proxy('http://www.pharmgkb.org/services/SearchService')
        -> search ($search_term);
    my $search_result = $soap_service->result;
    foreach my $search_obj(@{$search_result}) {
	if($search_obj->[1] =~ m/$key/ig) {
	    push(@pharm_id, $search_obj->[0]);
	}
    }
    return \@pharm_id;

}

1;


=head1 NAME

WWW::Search::PharmGKB - Search and retrieve information from the PharmGKB database

=head1 VERSION

Version 2.00

=cut

=head1 SYNOPSIS

    use WWW::Search::PharmGKB;
    use Data::Dumper;
    my $foo = WWW::Search::PharmGKB->new();
    my $search_result = $foo->gene_search('CYP2D6');
    print Dumper $search_result;


=head1 METHODS

=head2 new

=head3 Usage:

    $foo = WWW::Search::PharmGKB->new();
	    or
    $foo = new WWW::Search::PharmGKB;

=head3 Returns:

    Self

=cut

=head2 gene_search

=head3 Usage:

    $foo->gene_search();

=head3 Returns:

    A referenced hash. The keys are 'drugs', 'name', 'symbol', 'pathways',
    'drugs', 'diseases', 'phenotypes', 'alternate_names', 'alternate_symbols'

=head3 Note:

    all the keys contain referenced arrays as values. In the pathway value,
    the array has  key => value pairs 'pathway' => 'pharmGKB URL' as elements.
    All other keys have referenced array of PharmGKB IDs.

=cut

=head2 disease_search

=head3 Usage:

    $foo->disease_search();

=head3 Returns:

    A referenced hash of pharmGKB IDs. Each ID contains 'drugs', 'names', 'pathways', 'drugs',
    'genes', 'phenotypes'.

=head3 Note:

    all the keys contain referenced arrays as values. in the pathway value,
    the array has  key => value pairs 'pathway' => 'pharmGKB URL' as elements.
    All other keys have referenced array of PharmGKB IDs.
=cut

=head2 drug_search

=head3 Usage:

    $foo->drug_search();

=head3 Returns:

    A referenced hash of pharmGKB IDs. Each ID contains 'diseases', 'generic_names', 'trade_names',
    'pathways', 'genes', 'phenotypes', 'category', 'classification'

=head3 Note:

    all the keys contain referenced arrays as values. in the pathway value,
    the array has  key => value pairs 'pathway' => 'pharmGKB URL' as elements.
    All other keys have referenced array of PharmGKB IDs.
=cut

=head2 publication_search

=head3 Usage:

    $foo->publication_search();

=head3 Returns:

    A referenced hash of pharmGKB IDs. Each ID contains 'authors', 'page',
    'volume', 'month', 'grant_id', 'cross_reference', 'title', 'abstract', 'year',
    'journal'.

=cut

=head1 AUTHOR

Arun Venkataraman, C<<  >>

=head1 BUGS

Please report any bugs or feature requests to C, or through
the web interface at L.  I will be notified, and then you'll
automatically be notified of progress on your bug as I make changes.




=head1 SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc WWW::Search::PharmGKB

You can also look for information at:

=over 4

=item * RT: CPAN's request tracker

L

=item * AnnoCPAN: Annotated CPAN documentation

L

=item * CPAN Ratings

L

=item * Search CPAN

L

=back

You can contact the author for any issues or suggestions you come accross using this module.

=head1 ACKNOWLEDGEMENTS

This module is based on the perl client written by Andrew MacBride ([e-mail]) for PharmGKB's web services.

=head1 COPYRIGHT & LICENSE

Copyright 2010 Arun Venkataraman C, all rights reserved.

This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.


=cut