PathI - Interface for a path between ontology terms # see documentation of methods and an implementation, e.g., # Bio::Ontology::Path 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).

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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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email hlapp at gmx.net Additional contributors names and emails here 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)

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 L<Bio::Ontology::OntologyI> Args :