Bio::DB MeSH
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
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Summary
Bio::DB::MeSH - Term retrieval from a Web MeSH database
Package variables
Privates (from "my" definitions)
$ANALYSIS_SPEC = {name => 'MeSH term retrival', type => 'Entry retrieval'}
$URL = 'http://www.nlm.nih.gov/mesh/MBrowser.html'
$INPUT_SPEC = [ {mandatory=>'true', type => 'scalar', 'name'=> 'value', }, ]
$RESULT_SPEC = { '' => 'Bio::Phenotype::MeSH::Term', raw => 'raw output', }
Included modules
Bio::Phenotype::MeSH::Term
Bio::Phenotype::MeSH::Twig
Inherit
Bio::Tools::Analysis::SimpleAnalysisBase
Synopsis
 my $mesh = Bio::DB::MeSH->new();
my $term = $mesh->get_exact_term('Butter');
print $term->description;
Description
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.
Methods
_init
No description
Code
_webmodule
No description
Code
get_exact_termDescriptionCode
run
No description
Code
_cgi_url
No description
Code
_run
No description
Code
result
No description
Code
Methods description
get_exact_termcode    nextTop
  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.
Methods code
_initdescriptionprevnextTop
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 $self;
}
_webmoduledescriptionprevnextTop
sub _webmodule {
    my ($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;
    $self->{'_webmodule'} = 'Bio::Root::HTTPget';
    1;
}
get_exact_termdescriptionprevnextTop
sub get_exact_term {
    my ($self, $value) = @_;
    $self->{'_term'} = undef;
    $self->run($value) if $value;
    $self->throw("Could not connect to the server")
        unless $self->status eq 'COMPLETED';
    return $self->result;
}
rundescriptionprevnextTop
sub run {
    my ($self, $value) = @_;

    # check input
$self->throw("Need a MeSH name or ID as an input [$value]") if ref $value; # internal run()
$self->_run($value);
}
_cgi_urldescriptionprevnextTop
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='.$term;
}
_rundescriptionprevnextTop
sub _run {
    my ($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 $@; } $self->status('COMPLETED'); }
}
resultdescriptionprevnextTop
sub result {
    my ($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;
}
General documentation
SEE ALSOTop
Bio::Phenotype::MeSH::Term
FEEDBACKTop
Mailing ListsTop
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.
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Support Top
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 BugsTop
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/
AUTHORTop
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _