--- name: "Bio::Ontology::Relationship" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Ontology::Relationship" --- # Bio::Ontology::Relationship(3pm) a relationship for an ontology ## 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://github.com/bioperl/bioperl-live/issues ``` ## 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 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. ```