| Bio::Ontology::PathI(3pm) | User Contributed Perl Documentation | Bio::Ontology::PathI(3pm) |
Bio::Ontology::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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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)
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.
| 2021-08-15 | perl v5.32.1 |