Bio::Ontology::Relationship(3pm)			User Contributed Perl Documentation			  Bio::Ontology::Relationship(3pm)

NAME

       Bio::Ontology::Relationship - a relationship for an ontology

SYNOPSIS

	 $rel = Bio::Ontology::Relationship->new( -identifier	  => "16847",
						  -subject_term   => $subj,
						  -object_term	  => $obj,
						  -predicate_term => $pred );

DESCRIPTION

       This is a basic implementation of Bio::Ontology::RelationshipI.

       The terminology we use here is the one commonly used for ontologies, namely the triple of (subject, predicate, object), which in addition
       is scoped in a namespace (ontology). It is called triple because it is a tuple of three ontology terms.

       There are other terminologies in use for expressing relationships. For those who it helps to better understand the concept, the triple of
       (child, relationship type, parent) would be equivalent to the terminology chosen here, disregarding the question whether the notion of
       parent and child is sensible in the context of the relationship type or not. Especially in the case of ontologies with a wide variety of
       predicates the parent/child terminology and similar ones can quickly become ambiguous (e.g., A synthesises B), meaningless (e.g., A binds
       B), or even conflicting (e.g., A is-parent-of B), and are therefore strongly discouraged.

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://redmine.open-bio.org/projects/bioperl/

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

CONTRIBUTORS

	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	: $rel = Bio::Ontology::Relationship->new(-identifier	=> "16847",
							  -subject_term => $subject,
							  -object_term	=> $object,
							  -predicate_term => $type );
	Function: Creates a new Bio::Ontology::Relationship.
	Returns : A new Bio::Ontology::Relationship object.
	Args	: -identifier	  => the identifier of this relationship [scalar]
		  -subject_term   => the subject term [Bio::Ontology::TermI]
		  -object_term	  => the object term [Bio::Ontology::TermI]
		  -predicate_term => the predicate term [Bio::Ontology::TermI]

   init
	Title	: init()
	Usage	: $rel->init();
	Function: Initializes this Relationship to all undef.
	Returns :
	Args	:

   identifier
	Title	: identifier
	Usage	: $rel->identifier( "100050" );
		  or
		  print $rel->identifier();
	Function: Set/get for the identifier of this Relationship.
	Returns : The identifier [scalar].
	Args	: The identifier [scalar] (optional).

   subject_term
	Title	: subject_term
	Usage	: $rel->subject_term( $subject );
		  or
		  $subject = $rel->subject_term();
	Function: Set/get for the subject term of this Relationship.

		  The common convention for ontologies is to express
		  relationships between terms as triples (subject, predicate,
		  object).

	Returns : The subject term [Bio::Ontology::TermI].
	Args	: The subject term [Bio::Ontology::TermI] (optional).

   object_term
	Title	: object_term
	Usage	: $rel->object_term( $object );
		  or
		  $object = $rel->object_term();
	Function: Set/get for the object term of this Relationship.

		  The common convention for ontologies is to express
		  relationships between terms as triples (subject, predicate,
		  object).

	Returns : The object term [Bio::Ontology::TermI].
	Args	: The object term [Bio::Ontology::TermI] (optional).

   predicate_term
	Title	: predicate_term
	Usage	: $rel->predicate_term( $type );
		  or
		  $type = $rel->predicate_term();
	Function: Set/get for the predicate (relationship type) of this
		  relationship.

		  The common convention for ontologies is to express
		  relationships between terms as triples (subject, predicate,
		  object).

	Returns : The predicate term [Bio::Ontology::TermI].
	Args	: The predicate term [Bio::Ontology::TermI] (optional).

   ontology
	Title	: ontology
	Usage	: $ont = $obj->ontology()
	Function: Get/set the ontology that defined this relationship.
	Example :
	Returns : an object implementing L<Bio::Ontology::OntologyI>
	Args	: on set, undef or an object implementing
		  Bio::Ontology::OntologyI (optional)

       See Bio::Ontology::OntologyI.

   to_string
	Title	: to_string()
	Usage	: print $rel->to_string();
	Function: to_string method for Relationship.
	Returns : A string representation of this Relationship.
	Args	:

Deprecated Methods
	 These methods are deprecated and defined here solely to preserve
	 backwards compatibility.

perl v5.14.2							    2012-03-02					  Bio::Ontology::Relationship(3pm)