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://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

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.