Bio::Phenotype::MeSH::User(Contributed Perl DocumBio::Phenotype::MeSH::Term(3)NAMEBio::Phenotype::MeSH::Term - A MeSH term
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);
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.
SEE ALSO
Bio::DB::MeSH, Bio::Phenotype::MeSH::Twig
FEEDBACK
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:
http://bugzilla.open-bio.org/
AUTHOR
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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).
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).
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).
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).
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 :
purge_synonyms
Usage : $obj->purge_synonym();
Function: Deletes the list of synonyms to this term.
Returns : A list of scalars.
Args :
Twig management
Each MeSH term belongs to a complex tree like hierachy of terms where
each term can appear multiple times. The immediately surrounding nodes
of the tree are modelled in twigs.
See: Bio::Phenotype::MeSH::Twig.
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).
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 :
purge_twigs
Usage : $obj->purge_twig();
Function: Deletes the list of twigs associated with this term.
Returns : A list of scalars.
Args :
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 :
perl v5.14.1 2011-07-22 Bio::Phenotype::MeSH::Term(3)
