Bio::Ontology
RelationshipI
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Summary
RelationshipI - Interface for a relationship between ontology terms
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# see documentation of methods and an implementation, e.g.,
# Bio::Ontology::Relationship
Description
This is the minimal interface for a relationship between two terms in
an ontology. Ontology engines will use this.
The terminology we use here is the one commonly used for ontologies,
namely the triple of (subject, predicate, object), which in addition
is scoped in a namespace (ontology). It is called triple because it is
a tuple of three ontology terms.
There are other terminologies in use for expressing relationships. For
those who it helps to better understand the concept, the triple of
(child, relationship type, parent) would be equivalent to the
terminology chosen here, disregarding the question whether the notion
of parent and child is sensible in the context of the relationship
type or not. Especially in the case of ontologies with a wide variety
of predicates the parent/child terminology and similar ones can
quickly become ambiguous (e.g., A synthesises B), meaningless (e.g., A
binds B), or even conflicting (e.g., A is-parent-of B), and are
therefore strongly discouraged.
Methods
Methods description
Title : identifier
Usage : print $rel->identifier();
Function: Set/get for the identifier of this Relationship.
Note that this may not necessarily be used by a particular
ontology.
Returns : The identifier [scalar].
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 : ontology
Usage : $ont = $obj->ontology()
Function: Get the ontology that defined (is the scope for) this
relationship.
Example :
Returns : an object implementing Bio::Ontology::OntologyI
Args : |
Title : predicate_term
Usage : $type = $rel->predicate_term();
Function: Set/get for the relationship type of this relationship.
The common convention for ontologies is to express
relationships between terms as triples (subject, predicate,
object).
Returns : The relationship type [Bio::Ontology::TermI].
Args : |
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 : |
Methods code
sub identifier
{ shift->throw_not_implemented(); } | sub object_term
{ shift->throw_not_implemented(); } | sub ontology
{ shift->throw_not_implemented();
}
1; } | sub predicate_term
{ shift->throw_not_implemented(); } | sub subject_term
{ shift->throw_not_implemented(); } | General documentation
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| AUTHOR - Peter Dimitrov | Top |
Hilmar Lapp, email: hlapp at gmx.net
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _