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Bio::Annotation::OntolUsereContributed Perl DoBio::Annotation::OntologyTerm(3)

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(),"\n";
	  $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://github.com/bioperl/bioperl-live/issues

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 category 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 v5.32.1			  2019-12-07  Bio::Annotation::OntologyTerm(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Hilmar Lapp | APPENDIX | AnnotationI implementing functions | Methods for Bio::Ontology::TermI compliance

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