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.