Bio::Ontology::RelationshipI(3)            User Contributed Perl Documentation




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-lATbioperl.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-lATbioperl.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:

         http://bugzilla.open-bio.org/

AUTHOR - Peter Dimitrov
       Email dimitrovATgnf.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.



perl v5.12.2                                                 February 24, 2011