Bio::Annotation::OntologyTerm(3pm)			User Contributed Perl Documentation			Bio::Annotation::OntologyTerm(3pm)

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 = Bio::Annotation::Collection->new();

	  # this also implements a tag/value pair, where tag _and_ value are treated
	  # as ontology terms
	  my $annterm = Bio::Annotation::OntologyTerm->new(-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 ",$term->identifier(),
		"), ontology ",$term->ontology()->name(),"
";
	  $term = Bio::Ontology::Term->new(-name => 'ABC2',
					   -ontology => '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://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 - Hilmar Lapp
       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 = Bio::Annotation::OntologyTerm->new();
	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
		  -ontology.

AnnotationI implementing functions
   as_text
	Title	: as_text
	Usage	: my $text = $obj->as_text
	Function: Returns a textual representation of the annotation that
		  this object holds. Presently, it is tag name, name of the
		  term, and the is_obsolete attribute concatenated togather
		  with a delimiter (|).

	Returns : string
	Args	: none

   display_text
	Title	: display_text
	Usage	: my $str = $ann->display_text();
	Function: returns a string. Unlike as_text(), this method returns a string
		  formatted as would be expected for te specific implementation.

		  One can pass a callback as an argument which allows custom text
		  generation; the callback is passed the current instance and any text
		  returned
	Example :
	Returns : a string
	Args	: [optional] callback

   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 ontology() 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).

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

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

   add_synonym
	Title	: add_synonym
	Usage	: $term->add_synonym( @asynonyms );
		  or
		  $term->add_synonym( $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	:

   get_dblinks
	Title	: get_dblinks()
	Usage	: @ds = $term->get_dblinks();
	Function: Returns a list of each dblinks of this GO term.
	Returns : A list of dblinks [array of [scalars]].
	Args	:
	Note	: this is deprecated in favor of get_dbxrefs(), which works with strings
		  or L<Bio::Annotation::DBLink> instances

   get_dbxrefs
	Title	: get_dbxrefs()
	Usage	: @ds = $term->get_dbxrefs();
	Function: Returns a list of each dblinks of this GO term.
	Returns : A list of dblinks [array of [scalars] or Bio::Annotation::DBLink instances].
	Args	:

   add_dblink
	Title	: add_dblink
	Usage	: $term->add_dblink( @dbls );
		  or
		  $term->add_dblink( $dbl );
	Function: Pushes one or more dblinks
		  into the list of dblinks.
	Returns :
	Args	: One  dblink [scalar] or a list of
		   dblinks [array of [scalars]].
	Note	: this is deprecated in favor of add_dbxref(), which works with strings
		  or L<Bio::Annotation::DBLink> instances

   add_dbxref
	Title	: add_dbxref
	Usage	: $term->add_dbxref( @dbls );
		  or
		  $term->add_dbxref( $dbl );
	Function: Pushes one or more dblinks
		  into the list of dblinks.
	Returns :
	Args	:

   remove_dblinks
	Title	: remove_dblinks()
	Usage	: $term->remove_dblinks();
	Function: Deletes (and returns) the definition references of this GO term.
	Returns : A list of definition references [array of [scalars]].
	Args	:
	Note	: this is deprecated in favor of remove_dbxrefs(), which works with strings
		  or L<Bio::Annotation::DBLink> instances

   remove_dbxrefs
	Title	: remove_dbxrefs()
	Usage	: $term->remove_dbxrefs();
	Function: Deletes (and returns) the definition references of this GO term.
	Returns : A list of definition references [array of [scalars]].
	Args	:

   get_secondary_ids
	Title	: get_secondary_ids
	Usage	: @ids = $term->get_secondary_ids();
	Function: Returns a list of secondary identifiers of this Term.

		  Secondary identifiers mostly originate from merging terms,
		  or possibly also from splitting terms.

	Returns : A list of secondary identifiers [array of [scalar]]
	Args	:

   add_secondary_id
	Title	: add_secondary_id
	Usage	: $term->add_secondary_id( @ids );
		  or
		  $term->add_secondary_id( $id );
	Function: Adds one or more secondary identifiers to this term.
	Returns :
	Args	: One or more secondary identifiers [scalars]

   remove_secondary_ids
	Title	: remove_secondary_ids
	Usage	: $term->remove_secondary_ids();
	Function: Deletes (and returns) the secondary identifiers of this Term.
	Returns : The previous list of secondary identifiers [array of [scalars]]
	Args	:

perl v5.14.2							    2012-03-02					Bio::Annotation::OntologyTerm(3pm)