OBO::Core::RelationshipType - A type of relationship type in an ontology.
use OBO::Core::RelationshipType;
use strict;
# three new relationships types
my $r1 = OBO::Core::RelationshipType->new();
my $r2 = OBO::Core::RelationshipType->new();
my $r3 = OBO::Core::RelationshipType->new();
$r1->id("CCO:R0000001");
$r2->id("CCO:R0000002");
$r3->id("CCO:R0000003");
$r1->name("is a");
$r2->name("part of");
$r3->name("participates in");
# inverse
my $r3_inv = OBO::Core::RelationshipType->new();
$r3_inv->id("CCO:R0000004");
$r3_inv->name("has participant");
$r3_inv->inverse_of($r3);
# def as string
$r2->def_as_string("This is a dummy definition", "[CCO:vm, CCO:ls, CCO:ea \"Erick Antezana\"]");
my @refs_r2 = $r2->def()->dbxref_set()->get_set();
my %r_r2;
foreach my $ref_r2 (@refs_r2) {
$r_r2{$ref_r2->name()} = $ref_r2->name();
}
A type of relationship in the ontology.
Erick Antezana, <erant@psb.ugent.be>
Copyright (C) 2006, 2007, 2008 by Erick Antezana
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.
Usage - print $relationship_type->id() Returns - the relationship type ID Args - the relationship type ID Function - gets/sets an ID
Usage - print $relationship_type->name() Returns - the name of the relationship type Args - the name of the relationship type Function - gets/sets the name of the relationship type
Usage - $relationship_type->alt_id() or $relationship_type->alt_id($id1, $id2, $id3, ...) Returns - a set (OBO::Util::Set) with the alternate id(s) of this relationship type Args - the alternate id(s) (string) of this relationship type Function - gets/sets the alternate id(s) of this relationship type
Usage - $relationship_type->def() or $relationship_type->def($def) Returns - the definition (OBO::Core::Def) of the relationship type Args - the definition (OBO::Core::Def) of the relationship type Function - gets/sets the definition of the relationship type
Usage - $relationship_type->def_as_string() or $relationship_type->def_as_string("This is a sample", "[CCO:ea, PMID:9334324]")
Returns - the definition (string) of the relationship type
Args - the definition (string) of the relationship type plus the dbxref list describing the source of this definition
Function - gets/sets the definition of the relationship type
Usage - $relationship_type->namespace() or $relationship_type->namespace($ns1, $ns2, $ns3, ...) Returns - an array with the namespace to which this relationship type belongs Args - the namespacet(s) to which this relationship type belongs Function - gets/sets the namespace(s) to which this relationship type belongs
Usage - print $relationship_type->comment() Returns - the comment of this relationship type Args - the comment of this relationship type Function - gets/sets the comment of this relationship type
Usage - $relationship_type->subset() or $relationship_type->subset($ss1, $ss2, $ss3, ...) Returns - an array with the subset to which this relationship type belongs Args - the subset(s) to which this relationship type belongs Function - gets/sets the subset(s) to which this relationship type belongs
Usage - $relationship_type->synonym_set() or $relationship_type->synonym_set($synonym1, $synonym2, $synonym3, ...) Returns - an array with the synonym(s) of this relationship type Args - the synonym(s) of this relationship type Function - gets/sets the synonym(s) of this relationship type
Usage - print $relationship_type->synonym_as_string() or $relationship_type->synonym_as_string("this is a synonym text", "[CCO:ea]", "EXACT")
Returns - an array with the synonym(s) of this relationship type
Args - the synonym text (string), the dbxrefs (string), synonym scope (string) of this relationship type, and optionally the synonym type name (string)
Function - gets/sets the synonym(s) of this relationship type
Usage - $relationship_type->xref_set() or $relationship_type->xref_set($dbxref_set) Returns - a Dbxref set with the analogous xref(s) of this relationship type in another vocabulary Args - analogous xref(s) (OBO::Util::DbxrefSet) of this relationship type in another vocabulary Function - gets/sets the analogous xref(s) of this relationship type in another vocabulary
Usage - $relationship_type->xref_set_as_string() or $relationship_type->xref_set_as_string("[Reactome:20610, EC:2.3.2.12]")
Returns - the dbxref set with the analogous xref(s) of this relationship type; [] if the set is empty
Args - the dbxref set with the analogous xref(s) of this relationship type
Function - gets/sets the dbxref set with the analogous xref(s) of this relationship type
Usage - print $relationship_type->domain() or $relationship_type->domain($id1, $id2, $id3, ...) Returns - a set (OBO::Util::Set) with the domain(s) to which this relationship type belongs Args - the domain(s) (string) to which this relationship type belongs Function - gets/sets the domain(s) to which this relationship type belongs
Usage - print $relationship_type->range() or $relationship_type->range($id1, $id2, $id3, ...) Returns - a set (OBO::Util::Set) with the range(s) of this relationship type Args - the range(s) (string) of this relationship type Function - gets/sets the range(s) of this relationship type
Usage - $relationship_type->inverse_of() Returns - inverse relationship type of this relationship type Args - inverse relationship type of this relationship type Function - gets/sets the inverse relationship type of this relationship type
Usage - $relationship_type->is_cyclic() Returns - 1 (true) or 0 (false) Args - 1 (true) or 0 (false) Function - tells whether the relationship type is cyclic or not.
Usage - $relationship_type->is_reflexive() Returns - 1 (true) or 0 (false) Args - 1 (true) or 0 (false) Function - tells whether the relationship type is reflexive or not.
Usage - $relationship_type->is_symmetric() Returns - 1 (true) or 0 (false) Args - 1 (true) or 0 (false) Function - tells whether the relationship type is symmetric or not.
Usage - $relationship_type->is_anti_symmetric() Returns - 1 (true) or 0 (false) Args - 1 (true) or 0 (false) Function - tells whether the relationship type is anti symmetric or not.
Usage - $relationship_type->is_transitive() Returns - 1 (true) or 0 (false) Args - 1 (true) or 0 (false) Function - tells whether the relationship type is transitive or not.
Usage - $relationship_type->is_metadata_tag() Returns - 1 (true) or 0 (false) Args - 1 (true) or 0 (false) Function - tells whether this relationship type is a metadata tag or not.
Usage - $relationship_type->transitive_over() or $relationship_type->transitive_over($id1, $id2, $id3, ...) Returns - a set (OBO::Util::Set) with the relationship type(s) for which this relationship type is(are) transitive over Args - the relationship type(s) (OBO::Core::RelationshipType) with which this one is transitive over Function - gets/sets the set of the relationship type(s) for which this relationship type is(are) transitive over
Usage - print $relationship_type->is_obsolete() Returns - either 1 (true) or 0 (false) Args - either 1 (true) or 0 (false) Function - tells whether the relationship type is obsolete or not. 'false' by default.
Usage - $relationship_type->replaced_by() or $relationship_type->replaced_by($id1, $id2, $id3, ...) Returns - a set (OBO::Util::Set) with the id(s) of the replacing relationship type(s) Args - the the id(s) of the replacing relationship type(s) (string) Function - gets/sets the the id(s) of the replacing relationship type(s)
Usage - $relationship_type->consider() or $relationship_type->consider($id1, $id2, $id3, ...) Returns - a set (OBO::Util::Set) with the appropiate substitute(s) for an obsolete relationship type Args - the appropiate substitute(s) for an obsolete relationship type (string) Function - gets/sets the appropiate substitute(s) for this obsolete relationship type
Usage - $relationship_type->builtin() or $relationship_type->builtin(1) or $relationship_type->builtin(0) Returns - tells if this relationship type is builtin to the OBO format; false by default Args - 1 (true) or 0 (false) Function - gets/sets the value indicating whether this relationship type is builtin to the OBO format
Usage - print $relationship_type->equals($another_relationship_type) Returns - either 1 (true) or 0 (false) Args - the relationship type (OBO::Core::RelationshipType) to compare with Function - tells whether this relationship type is equal to the parameter
