Bio::DB::MeSH - Term retrieval from a Web MeSH database

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::DB::MeSH - Term retrieval from a Web MeSH database

SYNOPSIS

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 my $mesh = Bio::DB::MeSH->new();
 my $term = $mesh->get_exact_term('Butter');
 print $term->description;

DESCRIPTION

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This class retrieves a term from the Medical Subject Headings database by the National Library of Medicine of USA. See http://www.nlm.nih.gov/mesh/meshhome.html.

This class implements Bio::SimpleAnalysisI and wraps its methods under get_exact_term.

By default, web access uses WWW::Mechanize, but in its absence falls back to bioperl module Bio::WebAgent which is a subclass of LWP::UserAgent. If not even that is not installed, it uses Bio::Root::HTTPget.

SEE ALSO

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Bio::Phenotype::MeSH::Term

FEEDBACK

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Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR

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Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

get_exact_term

  Title   : get_exact_term
  Usage   : $s = $db->get_exact_term($value);
  Function: Retrive a single MeSH term using a unique ID or exact name.
  Example :
  Returns : a Bio::Phenotype::MeSH::Term object
  Args    : scalar, UID or name of a MeSH term

The returned term object contains information about the immediate vincinity of the term in the terminology hierarchy. See Bio::Phenotype::MeSH::Twig.

BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::DB::MeSH
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::DB::MeSH;
use strict;

use Bio::Phenotype::MeSH::Term;
use Bio::Phenotype::MeSH::Twig;

use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);


my $URL = 'http://www.nlm.nih.gov/mesh/MBrowser.html';

my $ANALYSIS_SPEC= {name => 'MeSH term retrival',
                    type => 'Entry retrieval'};
my $INPUT_SPEC = [
                  {mandatory=>'true',
                   type => 'scalar',
                   'name'=> 'value',
                  },
                 ];

my  $RESULT_SPEC =
    {
     '' => 'Bio::Phenotype::MeSH::Term',
     raw => 'raw output',
    };


sub _init {
    my $self = shift;
    $self->url($URL);
    $self->{'_ANALYSIS_SPEC'} =$ANALYSIS_SPEC;
    $self->{'_INPUT_SPEC'} =$INPUT_SPEC;
    $self->{'_RESULT_SPEC'} =$RESULT_SPEC;
    $self->{'_ANALYSIS_NAME'} = $ANALYSIS_SPEC->{'name'};
    $self->_webmodule;
    return $self;
}

sub _webmodule {
    my ($self) = shift;
    $self->{'_webmodule'} = '';
    eval {
        require WWW::Mechanize;
    };
    unless ($@) {
        $self->{'_webmodule'} = 'WWW::Mechanize';
        return;
    }
    eval {
        require LWP::UserAgent;
    };
    unless ($@) {
        $self->{'_webmodule'} = 'Bio::WebAgent';
        return;
    }
    require Bio::Root::HTTPget;
    $self->{'_webmodule'} = 'Bio::Root::HTTPget';
    1;
}



sub get_exact_term {
    my ($self, $value) = @_;
    $self->{'_term'} = undef;
    $self->run($value) if $value;
    $self->throw("Could not connect to the server")
        unless $self->status eq 'COMPLETED';
    return $self->result;
}


sub run {
    my ($self, $value) = @_;

    # check input
    $self->throw("Need a MeSH name or ID  as an input [$value]") if ref $value;

    # internal run()
    $self->_run($value);
}


sub _cgi_url {
  my($self, $field, $term) = @_;
  # we don't bother to URI::Escape $field and $term as this is an untainted private sub
  return 'http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?field='.$field.'&term='.$term;
}


sub  _run {
    my ($self, $value)  = @_;
    $self->throw('Need a value [$value]')
        unless $value;;
    # delay repeated calls by default by 3 sec, set delay() to change
#    $self->sleep;

    $self->status('TERMINATED_BY_ERROR');

    if ($self->{'_webmodule'} eq 'WWW::Mechanize') {
        $self->debug("using WWW::Mechanize...\n");
        my $agent = WWW::Mechanize->new();
        $agent->get($self->url);
        $agent->status == 200
            or $self->warn("Could not connect to the server\n") and return;

        $agent->form_name('MB');

        $agent->field("term", $value);
        if ($value =~ /\w\d{6}/) {
            $agent->field("field", 'uid');
        } else {
            $agent->field("field", 'entry');
        }
        $agent->click("exact");

        $self->{'_content'} = $agent->content();
        $self->status('COMPLETED');
        return;
    }
    elsif ($self->{'_webmodule'} eq 'Bio::WebAgent') {
        $self->debug("using LWP::UserAgent...\n");
        my $response;
        if ($value =~ /\w\d{6}/) {
            $self->{'_content'} =
                $response = eval {
                    $self->get( $self->_cgi_url('uid', $value) )
                };
            $self->warn("Could not connect to the server\n") and return
                if $@;
        } else {
            $self->{'_content'} =
                eval {
                    $response = $self->get( $self->_cgi_url('entry', $value) )
                };
            $self->warn("Could not connect to the server\n") and return
                if $@;
        }
        if ($response->is_success) {
            $self->{'_content'} =  $response->content;
            $self->status('COMPLETED');
        }
        return;
    } else {
        $self->debug("using Bio::Root::HTTPget...\n");
        my $agent = Bio::Root::HTTPget->new();
        if ($value =~ /\w\d{6}/) {
            $self->{'_content'} =
                eval {
                    $agent->get( $self->_cgi_url('uid', $value) )
                };
            $self->warn("Could not connect to the server\n") and return
                if $@;
        } else {
            $self->{'_content'} =
                eval {
                    $agent->get( $self->_cgi_url('entry', $value) )
                };
            $self->debug("Could not connect to the server\n") and return
                if $@;
        }
        $self->status('COMPLETED');
    }
}

sub result {
    my ($self,$value) = @_;

    $self->throw("Could not retrive results") unless $self->status('COMPLETED');

    # no processing
    return $self->{'_content'} if $value && $value eq 'raw';


    # create a MeSH::Term object
    $_ = $self->{'_content'};
    $self->debug( substr($_, 0, 100) . "\n");
    my ($id) = m|Unique ID</TH><TD>(.*?)</TD>|i;
    my ($name) = m|MeSH Heading</TH><TD>([^<]+)|i;
    my ($desc) = m|Scope Note</TH><TD>(.*?)</TD>|is;
    $self->throw("No description returned: $_") unless defined $desc;
    $desc =~ s/<.*?>//sg;
	$desc =~ s/\n/ /g;

    my $term = Bio::Phenotype::MeSH::Term->new(-id => $id,
                                               -name => $name,
                                               -description => $desc
                                              );
    my ($trees) = $self->{'_content'} =~ /MeSH Tree Structures(.*)/s;

    while (m|Entry Term</TH><TD>([^<]+)|ig) {
        $term->add_synonym($1);
        $self->debug("Synonym: |$1|\n");
    }

    foreach (split /<HR>/i, $trees ) {
        next unless /$name/;
        s/<TD.*?>/ /sgi;
        s/<.*?>//sg;
        s/&nbsp;/ /sg;
        #print "|$_|";
        my ($treeno) = /$name \[([^]]+)]/;
        my ($parent_treeno) = $treeno =~ /(.*)\.\d{3}/;
        my ($parent) =  /\n +(\w.+) \[$parent_treeno\]/;

        my $twig = Bio::Phenotype::MeSH::Twig->new(-parent => $parent);
        $term->add_twig($twig);

        $self->debug("Parent: |$parent|\n");
        while (/\n +(\w.+) \[$treeno\./g ) {
            $twig->add_child($1);
            $self->debug("Child: |$1|\n");
        }

        while (/\n +(\w.+) \[$parent_treeno\./g ) {
            next if $name eq $1;
            $twig->add_sister($1);
            $self->debug("Sister: |$1|\n");
        }
    }
    return $term;
}

1;