Bio::Ontology PathI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Ontology::PathI - Interface for a path between ontology terms
Package variables
No package variables defined.
    # 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).
Methods description
distancecode    nextTop
 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)
Methods code
sub distance {
    return shift->throw_not_implemented();
General documentation
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AUTHOR - Hilmar LappTop
Email hlapp at
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Ontology::RelationshipI MethodsTop
 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 :
 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 :
 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 :
 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.