Bio::Phenotype::MeSH::Term(3pm) 			User Contributed Perl Documentation			   Bio::Phenotype::MeSH::Term(3pm)

NAME

       Bio::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:

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

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 hierarchy 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 v5.14.2							    2012-03-02					   Bio::Phenotype::MeSH::Term(3pm)