Bio::Ontology::Relationship(3pm) User Contributed Perl Documentation Bio::Ontology::Relationship(3pm)
NAME
Bio::Ontology::Relationship - a relationship for an ontology
SYNOPSIS
$rel = Bio::Ontology::Relationship->new( -identifier => "16847",
-subject_term => $subj,
-object_term => $obj,
-predicate_term => $pred );
DESCRIPTION
This is a basic implementation of Bio::Ontology::RelationshipI.
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.
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 lists 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 the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
CONTRIBUTORS
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 _
new
Title : new
Usage : $rel = Bio::Ontology::Relationship->new(-identifier => "16847",
-subject_term => $subject,
-object_term => $object,
-predicate_term => $type );
Function: Creates a new Bio::Ontology::Relationship.
Returns : A new Bio::Ontology::Relationship object.
Args : -identifier => the identifier of this relationship [scalar]
-subject_term => the subject term [Bio::Ontology::TermI]
-object_term => the object term [Bio::Ontology::TermI]
-predicate_term => the predicate term [Bio::Ontology::TermI]
init
Title : init()
Usage : $rel->init();
Function: Initializes this Relationship to all undef.
Returns :
Args :
identifier
Title : identifier
Usage : $rel->identifier( "100050" );
or
print $rel->identifier();
Function: Set/get for the identifier of this Relationship.
Returns : The identifier [scalar].
Args : The identifier [scalar] (optional).
subject_term
Title : subject_term
Usage : $rel->subject_term( $subject );
or
$subject = $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 : The subject term [Bio::Ontology::TermI] (optional).
object_term
Title : object_term
Usage : $rel->object_term( $object );
or
$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 : The object term [Bio::Ontology::TermI] (optional).
predicate_term
Title : predicate_term
Usage : $rel->predicate_term( $type );
or
$type = $rel->predicate_term();
Function: Set/get for the predicate (relationship type) of this
relationship.
The common convention for ontologies is to express
relationships between terms as triples (subject, predicate,
object).
Returns : The predicate term [Bio::Ontology::TermI].
Args : The predicate term [Bio::Ontology::TermI] (optional).
ontology
Title : ontology
Usage : $ont = $obj->ontology()
Function: Get/set the ontology that defined this relationship.
Example :
Returns : an object implementing L<Bio::Ontology::OntologyI>
Args : on set, undef or an object implementing
Bio::Ontology::OntologyI (optional)
See Bio::Ontology::OntologyI.
to_string
Title : to_string()
Usage : print $rel->to_string();
Function: to_string method for Relationship.
Returns : A string representation of this Relationship.
Args :
Deprecated Methods
These methods are deprecated and defined here solely to preserve
backwards compatibility.
perl v5.14.2 2012-03-02 Bio::Ontology::Relationship(3pm)