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Bio::Ontology::RelatioUserpContributed Perl Bio::Ontology::RelationshipType(3)

NAME
       Bio::Ontology::RelationshipType	- a relationship type for an ontology

SYNOPSIS
	 #

DESCRIPTION
       This class can be used to model various types of	relationships (such as
       "IS_A", "PART_OF", "CONTAINS", "FOUND_IN", "RELATED_TO").

       This class extends Bio::Ontology::Term, so it essentially is-a
       Bio::Ontology::TermI. In	addition, all methods are overridden such as
       to make the object immutable.

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:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR
       Christian M. Zmasek

       Email: czmasek-at-burnham.org  or  cmzmasek@yahoo.com

       WWW:   http://monochrome-effect.net/

       Address:

	 Genomics Institute of the Novartis Research Foundation
	 10675 John Jay	Hopkins	Drive
	 San Diego, CA 92121

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

   get_instance
	Title	: get_instance
	Usage	: $IS_A	      =	Bio::Ontology::RelationshipType->get_instance( "IS_A" );
		  $PART_OF    =	Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
		  $RELATED_TO =	Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" );
		  $CONTAINS   =	Bio::Ontology::RelationshipType->get_instance( "CONTAINS" );
		  $FOUND_IN   =	Bio::Ontology::RelationshipType->get_instance( "FOUND_IN" );
	Function: Factory method to create instances of	RelationshipType
	Returns	: [Bio::Ontology::RelationshipType]
	Args	: "IS_A" or "PART_OF" or "CONTAINS" or "FOUND_IN" or
		  "RELATED_TO" [scalar]
		  the ontology [Bio::Ontology::OntologyI] (optional)

   init
	Title	: init()
	Usage	: $type->init();
	Function: Initializes this to all undef	and empty lists.
	Returns	:
	Args	:

   equals
	Title	: equals
	Usage	: if ( $type->equals( $other_type ) ) {	...
	Function: Compares this	type to	another	one, based on string "eq" of
		  the "identifier" field, if at	least one of the two types has
		  the identifier set, or string	eq of the name otherwise.
	Returns	: true or false
	Args	: [Bio::Ontology::RelationshipType]

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

   name
	Title	: name
	Usage	: $term->name( "is a type" );
		  or
		  print	$term->name();
	Function: Set/get for the immutable name of this Type.
	Returns	: The name [scalar].
	Args	: The name [scalar] (optional).

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

   ontology
	Title	: ontology
	Usage	: $term->ontology( $top	);
		  or
		  $top = $term->ontology();
	Function: Set/get for the ontology this	relationship type lives	in.
	Returns	: The ontology [Bio::Ontology::OntologyI].
	Args	: On set, the ontology [Bio::Ontology::OntologyI] (optional).

   version
	Title	: version
	Usage	: $term->version( "1.00" );
		  or
		  print	$term->version();
	Function: Set/get for immutable	version	information.
	Returns	: The version [scalar].
	Args	: The version [scalar] (optional).

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

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

Private	methods
       May be overridden in a derived class, but should	never be called	from
       outside.

   veto_change
	Title	: veto_change
	Usage	:
	Function: Called if an attribute is changed. Setting an	attribute is
		  considered a change if it had	a value	before and the attempt
		  to set it would change the value.

		  This method returns the message to be	printed	in the exception.

	Example	:
	Returns	: A string
	Args	: The name of the attribute that was attempted to change.
		  Optionally, the old value and	the new	value for reporting
		  purposes only.

perl v5.32.1			  2019-12-07Bio::Ontology::RelationshipType(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | APPENDIX | Private methods

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