Bio::Phenotype::MeSH::Term - A MeSH term 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); 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. Bio::DB::MeSH, Bio::Phenotype::MeSH::Twig

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Heikki Lehvaslaiho, heikki@ebi.ac.uk 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 :