#
# BioPerl module for Bio::Phenotype::MeSH::Term
#
# 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
=head1 NAME
Bio::Phenotype::MeSH::Term - A MeSH term
=head1 SYNOPSIS
use Bio::Phenotype::MeSH::Term;
# create a term object
my $term = Bio::Phenotype::MeSH::Term->new
(-id => 'D000001',
-name => 'Dietary Fats',
-description => 'dietary fats are...'
);
# get a Bio::Phenotype::MeSH::Twig somehow...
$term->add_twig($twig1);
=head1 DESCRIPTION
This class keeps information about MeSH terms. MeSH stands for Medical
Subject Headings and is one of the ways for annotaing biomedical
literature. The terminology is maintained by National Library of
Medicine of USA . See http://www.nlm.nih.gov/mesh/meshhome.html.
In addition to id, name and description a term can know about its
surrounding terms (Bio::Phenotype::MeSH::Twig) in the term hierarchy.
This class is mainly used from Bio::DB::MeSH which retrieves terms
over the Web.
=head1 SEE ALSO
L<Bio::DB::MeSH>,
L<Bio::Phenotype::MeSH::Twig>
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHOR
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Phenotype::MeSH::Term;
use strict;
use base qw(Bio::Root::Root);
sub new {
my( $class,@args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $id, $name, $description, $comment ) = $self->_rearrange
( [ qw( ID
NAME
DESCRIPTION
SPECIES
COMMENT
) ],
@args );
$self->{"_twigs"} = [];
$id && $self->id( $id );
$name && $self->name( $name );
$description && $self->description( $description );
return $self;
}
=head2 id
Title : id
Usage : $obj->id( "r1" );
or
print $obj->id();
Function: Set/get for the id.
Returns : A id [scalar].
Args : A id [scalar] (optional).
=cut
sub id {
my ( $self, $value ) = @_;
$self->{ "_id" } = $value if defined $value;
return $self->{ "_id" };
}
=head2 name
Title : name
Usage : $obj->name( "r1" );
or
print $obj->name();
Function: Set/get for the name.
Returns : A name [scalar].
Args : A name [scalar] (optional).
=cut
sub name {
my ( $self, $value ) = @_;
$self->{ "_name" } = $value if defined $value;
return $self->{ "_name" };
}
=head2 description
Title : description
Usage : $obj->description( "r1" );
or
print $obj->description();
Function: Set/get for the description.
Returns : A description [scalar].
Args : A description [scalar] (optional).
=cut
sub description {
my ( $self, $value ) = @_;
$self->{ "_description" } = $value if defined $value;
return $self->{ "_description" };
}
=head2 add_synonym
Title : add_synonym
Usage : $obj->add_synonym( @synonyms );
or
$obj->add_synonym( $synonym );
Function: Pushes one or more synonyms for the term term
into the list of synonyms.
Returns :
Args : scalar(s).
=cut
sub add_synonym {
my ( $self, @values ) = @_;
push( @{ $self->{ "_synonyms" } }, @values );
}
=head2 each_synonym
Title : each_synonym()
Usage : @gs = $obj->each_synonym();
Function: Returns a list of gene symbols [scalars, most likely Strings]
associated with this phenotype.
Returns : A list of scalars.
Args :
=cut
sub each_synonym {
my ( $self ) = shift;
return @{ $self->{ "_synonyms" } };
}
=head2 purge_synonyms
Usage : $obj->purge_synonym();
Function: Deletes the list of synonyms to this term.
Returns : A list of scalars.
Args :
=cut
sub purge_synonyms {
my ( $self ) = @_;
$self->{ "_synonyms" } = [];
}
=head2 Twig management
Each MeSH term belongs to a complex tree like hierarchy of terms where
each term can appear multiple times. The immediately surrounding nodes
of the tree are modelled in twigs.
See: L<Bio::Phenotype::MeSH::Twig>.
=cut
=head2 add_twig
Title : add_twig
Usage : $obj->add_twig( @twigs );
or
$obj->add_twig( $twig );
Function: Pushes one or more twig term names [scalars, most likely Strings]
into the list of twigs.
Returns :
Args : scalar(s).
=cut
sub add_twig {
my ( $self, @values ) = @_;
foreach my $twig (@values) {
$self->warn ("Not a MeSH twig [$twig]")
unless $twig->isa('Bio::Phenotype::MeSH::Twig');
$twig->term($self);
push( @{ $self->{ "_twigs" } }, $twig );
}
1;
}
=head2 each_twig
Title : each_twig()
Usage : @gs = $obj->each_twig();
Function: Returns a list of gene symbols [scalars, most likely Strings]
associated with this phenotype.
Returns : A list of scalars.
Args :
=cut
sub each_twig {
my ( $self ) = shift;
return @{ $self->{ "_twigs" } };
}
=head2 purge_twigs
Usage : $obj->purge_twig();
Function: Deletes the list of twigs associated with this term.
Returns : A list of scalars.
Args :
=cut
sub purge_twigs {
my ( $self ) = @_;
$self->{ "_twigs" } = [];
}
=head2 each_parent
Title : each_parent()
Usage : @gs = $obj->each_parent();
Function: Returns a list of names of parents for this term
Returns : A list of scalars.
Args :
=cut
sub each_parent {
my ( $self ) = shift;
return map {$_->parent()} @{ $self->{ "_twigs" } };
}
1;