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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:

   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    :