Bio::Ontology::RelationshipI - Interface for a relationship between ontology
terms
# see documentation of methods and an implementation, e.g.,
# Bio::Ontology::Relationship
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.
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.
[email protected] - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
[email protected]
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.
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
Email
[email protected]
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 _
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 : 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 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 : 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 :
See Bio::Ontology::OntologyI.