Bio::Ontology
PathI
Toolbar
Summary
PathI - Interface for a path between ontology terms
Package variables
No package variables defined.
Included modules
Inherit
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).
Methods
Methods description
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
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/MailList.shtml - About the mailing lists
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 _
| Bio::Ontology::RelationshipI Methods | Top |
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 :