go::model::relationship(3pm) [debian man page]
GO::Model::Relationship(3pm) User Contributed Perl Documentation GO::Model::Relationship(3pm) NAME
GO::Model::Relationship - relationship between two terms SYNOPSIS
DESCRIPTION
a relationship between two GO::Model::Terms relationships can be thought of as statements or sentences of the form SUBJECT-TERM PREDICATE OBJECT-TERM for example, "dog" IS_A "animal" "G-Protein coupled receptor" IS_A "transmembrane receptor" Statements have a subject (i.e. the subject of the sentence/statement), a predicate/relationship-type and an object (i.e. the object of the sentence/statement) Relationships can also be seen as arcs in a directed graph, with the subject being equivalent to the child, and the object equivalent to the parent. The arc is labeled with the predicate/relationship-type. A Relationship object currently does not contain an actual pointer to a GO::Model::Term object. Instead it stores the ID of that term. This is intended to be used in conjunction with the Graph object, or with the database. subject_acc Title : subject_acc Usage : $obj->subject_acc($newid) Usage : $currid = $obj->subject_acc() Synonyms: subj_acc, acc2, child_acc Function: gets or sets the identifier for the child/subject term Example : Returns : value of subject_acc (string) Args : on set, new value (string) All Relationships can be thought of "subject-predicate-object" statements. The statement is *about* the subject, and states something about the relationship *to* the object. For example, the if we have a Relationship: cell ^ | | [part_of] | cell nucleus This is a statement about cell nuclei in general, so "cell nucleus" is the subject (sometimes called the child node). The Relationship tells us that all cell nuclei are part_of some cell, so the object of the relationship (sometimes called the parent node) is "cell" object_acc Title : object_acc Usage : $obj->object_acc($newid) Usage : $currid = $obj->object_acc() Synonyms: obj_acc, acc1, parent_acc Function: gets or sets the identifier for the parent/object term Example : Returns : value of object_acc (string) Args : on set, new value (string) See Also: subj_acc type Title : type Usage : $obj->type($newval) Usage : $currval = $obj->type() Synonyms: Function: gets or sets the relationship type (a string) Example : Returns : value of type (string) Args : on set, new value (string) Currently any string is allowed; in future the type string may be constrained to come from a controlled vocabulary of relationship types perl v5.14.2 2013-02-07 GO::Model::Relationship(3pm)
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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)