table of contents
Bio::Ontology::PathI(3pm) | User Contributed Perl Documentation | Bio::Ontology::PathI(3pm) |
NAME¶
Bio::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:
https://github.com/bioperl/bioperl-live/issues
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.
2021-08-15 | perl v5.32.1 |