bionic (3) Bio::Phenotype::MeSH::Term.3pm.gz

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://github.com/bioperl/bioperl-live/issues

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    :