Provided by: libbio-perl-perl_1.7.6-3_all bug

NAME

       Bio::Ontology::RelationshipI - Interface for a relationship between ontology terms

SYNOPSIS

           # see documentation of methods and an implementation, e.g.,
           # Bio::Ontology::Relationship

DESCRIPTION

       This is the minimal interface for a relationship between two terms in an ontology.
       Ontology engines will use this.

       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 list.  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 of the bugs and their
       resolution. Bug reports can be submitted via the web:

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

AUTHOR - Peter Dimitrov

       Email dimitrov@gnf.org

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 _

   identifier
        Title   : identifier
        Usage   : print $rel->identifier();
        Function: Set/get for the identifier of this Relationship.

                  Note that this may not necessarily be used by a particular
                  ontology.

        Returns : The identifier [scalar].
        Args    :

   subject_term
        Title   : subject_term
        Usage   : $subj = $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    :

   object_term
        Title   : object_term
        Usage   : $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    :

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

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

        Returns : The relationship type [Bio::Ontology::TermI].
        Args    :

   ontology
        Title   : ontology
        Usage   : $ont = $obj->ontology()
        Function: Get the ontology that defined (is the scope for) this
                  relationship.
        Example :
        Returns : an object implementing Bio::Ontology::OntologyI
        Args    :

       See Bio::Ontology::OntologyI.