NAME

Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI

SYNOPSIS

   use Bio::Annotation::OntologyTerm;
   use Bio::Annotation::Collection;
   use Bio::Ontology::Term;

   my $coll = new Bio::Annotation::Collection;

   # this also implements a tag/value pair, where tag _and_ value are treated
   # as ontology terms
   my $annterm = new Bio::Annotation::OntologyTerm(-label => 'ABC1',
                                                   -tagname => 'Gene Name');
   # ontology terms can be added directly - they implicitly have a tag
   $coll->add_Annotation($annterm);

   # implementation is by composition - you can get/set the term object
   # e.g.
   my $term = $annterm->term(); # term is-a Bio::Ontology::TermI
   print "ontology term ",$term->name()," (ID ",$term->identifier(),
         "), category ",$term->category()->name(),"\n";
   $term = Bio::Ontology::Term->new(-name => 'ABC2', -category => 'Gene Name');
   $annterm->term($term);

DESCRIPTION

Ontology term annotation object

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 one of 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@bioperl.org
  http://bugzilla.bioperl.org/

AUTHOR - Hilmar Lapp

Email bioperl-l@bio.perl.org Email hlapp at gmx.net

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $sv = new Bio::Annotation::OntologyTerm;
 Function: Instantiate a new OntologyTerm object
 Returns : Bio::Annotation::OntologyTerm object
 Args    : -term => $term to initialize the term data field [optional]
           Most named arguments that Bio::Ontology::Term accepts will work
           here too. -label is a synonym for -name, -tagname is a synonym for
           -category.

AnnotationI implementing functions

as_text

 Title   : as_text
 Usage   : my $text = $obj->as_text
 Function: return the string "Name: $v" where $v is the name of the term
 Returns : string
 Args    : none

hash_tree

 Title   : hash_tree
 Usage   : my $hashtree = $value->hash_tree
 Function: For supporting the AnnotationI interface just returns the value
           as a hashref with the key 'value' pointing to the value
 Returns : hashrf
 Args    : none

tagname

 Title   : tagname
 Usage   : $obj->tagname($newval)
 Function: Get/set the tagname for this annotation value.

           Setting this is optional. If set, it obviates the need to provide
           a tag to AnnotationCollection when adding this object.

           This is aliased to category() here.
 Example : 
 Returns : value of tagname (a scalar)
 Args    : new value (a scalar, optional)

Methods for Bio::Ontology::TermI compliance

term

 Title   : term
 Usage   : $obj->term($newval)
 Function: Get/set the Bio::Ontology::TermI implementing object.

           We implement TermI by composition, and this method sets/gets the
           object we delegate to.
 Example : 
 Returns : value of term (a Bio::Ontology::TermI compliant object)
 Args    : new value (a Bio::Ontology::TermI compliant object, optional)

identifier

 Title   : identifier
 Usage   : $term->identifier( "0003947" );
           or
           print $term->identifier();
 Function: Set/get for the identifier of this Term.
 Returns : The identifier [scalar].
 Args    : The identifier [scalar] (optional).

name

 Title   : name
 Usage   : $term->name( "N-acetylgalactosaminyltransferase" );
           or
           print $term->name();
 Function: Set/get for the name of this Term.
 Returns : The name [scalar].
 Args    : The name [scalar] (optional).

definition

 Title   : definition
 Usage   : $term->definition( "Catalysis of ..." );
           or
           print $term->definition();
 Function: Set/get for the definition of this Term.
 Returns : The definition [scalar].
 Args    : The definition [scalar] (optional).

category

 Title   : category
 Usage   : $term->category( $top );
           or 
           $top = $term->category();
 Function: Set/get for a relationship between this Term and
           another Term (e.g. the top level of the ontology).
 Returns : The category of this Term [TermI].
 Args    : The category of this Term [TermI or scalar -- which
           becomes the name of the catagory term] (optional).

is_obsolete

 Title   : is_obsolete
 Usage   : $term->is_obsolete( 1 );
           or
           if ( $term->is_obsolete() )
 Function: Set/get for the obsoleteness of this Term.
 Returns : the obsoleteness [0 or 1].
 Args    : the obsoleteness [0 or 1] (optional).

comment

 Title   : comment
 Usage   : $term->comment( "Consider the term ..." );
           or 
           print $term->comment();
 Function: Set/get for an arbitrary comment about this Term.
 Returns : A comment.
 Args    : A comment (optional).

each_synonym

 Title   : each_synonym()
 Usage   : @aliases = $term->each_synonym();                 
 Function: Returns a list of aliases of this Term.
 Returns : A list of aliases [array of [scalar]].
 Args    :

add_synonyms

 Title   : add_synonyms
 Usage   : $term->add_synonyms( @asynonyms );
           or
           $term->add_synonyms( $synonym );                  
 Function: Pushes one or more synonyms into the list of synonyms.
 Returns : 
 Args    : One synonym [scalar] or a list of synonyms [array of [scalar]].

remove_synonyms

 Title   : remove_synonyms()
 Usage   : $term->remove_synonyms();
 Function: Deletes (and returns) the synonyms of this Term.
 Returns : A list of synonyms [array of [scalar]].
 Args    :

cpanm LocalConfig

perl -MCPAN -e shell
install LocalConfig