Bio::Ontology::PathI(3User Contributed Perl DocumentatiBio::Ontology::PathI(3)NAMEBio::Ontology::PathI - Interface for a path between ontology terms
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).
FEEDBACK
Mailing Lists
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/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and
data examples if at all possible.
Reporting Bugs
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 the
web:
http://bugzilla.open-bio.org/
AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
APPENDIX
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)
Bio::Ontology::RelationshipI Methods
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 Bio::Ontology::OntologyI
Args :
See Bio::Ontology::OntologyI.
perl v5.14.1 2011-07-22 Bio::Ontology::PathI(3)
