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

NAME

       Bio::Ontology::PathI - Interface for a path between ontology terms

SYNOPSIS

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

DESCRIPTION

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

       Essentially this is a very thin extension of the Bio::Ontology::RelationshipI interface.
       It basically adds an attribute distance(). For a RelationshipI, you can think of distance
       as equal to zero (subject == object) or 1 (subject != object).

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 - 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 _

   distance
        Title   : distance
        Usage   : $obj->distance($newval)
        Function: Get (and set if the implementation allows it) the distance
                  between the two terms connected by this path.

        Example :
        Returns : value of distance (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

Bio::Ontology::RelationshipI Methods

   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 predicate of this relationship.

                  For a path the predicate (relationship type) is defined as
                  the greatest common denominator of all predicates
                  (relationship types) encountered along the path. I.e., if
                  predicate A is-a predicate B, the greatest common
                  denominator for a path containing both predicates A and B is B

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

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

       See Bio::Ontology::OntologyI.