Usage - print $relationship_type->id() Returns - the relationship type ID Args - the relationship type ID Function - gets/sets an ID
Usage - print $relationship_type->is_anonymous() or $relationship_type->is_anonymous("1") Returns - either 1 (true) or 0 (false) Args - either 1 (true) or 0 (false) Function - tells whether this relationship type is anonymous or not.
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", "[APO: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 Remark - make sure that colons (,) are scaped (\,) when necessary
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 Remark1 - if the synonym (text) is already in the set of synonyms of this relationship type, its scope (and their dbxref's) will be updated (provided they have the same synonym type name) Remark2 - a synonym text identical to the relationship type name is not added to the set of synonyms of this relationship type
Usage - print $relationship_type->synonym_as_string() or $relationship_type->synonym_as_string("this is a synonym text", "[APO: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 Remark1 - if the synonym (text) is already in the set of synonyms of this relationship type, its scope (and their dbxref's) will be updated (provided they have the same synonym type name) Remark2 - a synonym text identical to the relationship type name is not added to the set of synonyms 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 Remark - make sure that colons (,) are scaped (\,) when necessary
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() or $relationship_type->inverse_of($inv_rel) Returns - inverse relationship type (OBO::Core::RelationshipType) of this relationship type Args - inverse relationship type (OBO::Core::RelationshipType) 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->is_class_level() Returns - 1 (true) or 0 (false) Args - 1 (true) or 0 (false) Function - tells whether this relationship type is a class-level relation 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) (string) 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 - $relationship_type->holds_over_chain() or $relationship_type->holds_over_chain($rt1, $rt2) Returns - an array of pairs (string) with the relationship type identifiers for which this relationship type holds over a chain Args - the relationship type identifiers (string) with which this one holds over a chain Function - gets/sets the set of the relationship types for which this relationship type holds over a chain
Usage - $relationship_type->is_functional() or $relationship_type->is_functional(1) or $relationship_type->is_functional(0) Returns - tells if this relationship type is functional; false by default Args - 1 (true) or 0 (false) Function - gets/sets the value indicating whether this relationship type is functional
Usage - $relationship_type->is_inverse_functional() or $relationship_type->is_inverse_functional(1) or $relationship_type->is_inverse_functional(0) Returns - tells if this relationship type is inverse functional; false by default Args - 1 (true) or 0 (false) Function - gets/sets the value indicating whether this relationship type is inverse functional
Usage - $relationship_type->intersection_of() or $relationship_type->intersection_of($t1, $t2, $r1, ...) Returns - an array with the terms/relations which define this relationship type Args - a set (strings) of terms/relations which define this relationship type Function - gets/sets the set of terms/relatonships defining this relationship type
Usage - $relationship_type->union_of() or $relationship_type->union_of($t1, $t2, $r1, ...) Returns - an array with the terms/relations which define this relationship type Args - a set (strings) of terms/relations which define this relationship type Function - gets/sets the set of terms/relatonships defining this relationship type
Usage - $relationship_type->disjoint_from() or $relationship_type->disjoint_from($disjoint_term_id1, $disjoint_term_id2, $disjoint_term_id3, ...) Returns - the disjoint relationship type id(s) (string(s)) from this one Args - the relationship type id(s) (string) that is (are) disjoint from this one Function - gets/sets the disjoint relationship type(s) from this one
Usage - print $relationship_type->created_by() or $relationship_type->created_by("erick_antezana") Returns - name (string) of the creator of the relationship type, may be a short username, initials or ID Args - name (string) of the creator of the relationship type, may be a short username, initials or ID Function - gets/sets the name of the creator of the relationship type
Usage - print $relationship_type->creation_date() or $relationship_type->creation_date("2010-04-13T01:32:36Z") Returns - date (string) of creation of the relationship type specified in ISO 8601 format Args - date (string) of creation of the relationship type specified in ISO 8601 format Function - gets/sets the date of creation of the relationship type
Usage - print $relationship_type->modified_by() or $relationship_type->modified_by("erick_antezana") Returns - name (string) of the modificator of the relationship type, may be a short username, initials or ID Args - name (string) of the modificator of the relationship type, may be a short username, initials or ID Function - gets/sets the name of the modificator of the relationship type
Usage - print $relationship_type->modification_date() or $relationship_type->modification_date("2010-04-13T01:32:36Z") Returns - date (string) of modification of the relationship type specified in ISO 8601 format Args - date (string) of modification of the relationship type specified in ISO 8601 format Function - gets/sets the date of modification of the relationship type
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
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("APO:R0000001");
$r2->id("APO:R0000002");
$r3->id("APO:R0000003");
$r1->name("is a");
$r2->name("part of");
$r3->name("participates in");
# rel. type creator + date
$r1->created_by("erick_antezana");
$r1->creation_date("2008-04-13T01:32:36Z ");
# inverse
my $r3_inv = OBO::Core::RelationshipType->new();
$r3_inv->id("APO:R0000004");
$r3_inv->name("has participant");
$r3_inv->inverse_of($r3);
# def as string
$r2->def_as_string("This is a dummy definition", '[APO:vm, APO:ls, APO: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, <erick.antezana -@- gmail.com>
Copyright (c) 2006-2015 by Erick Antezana. All rights reserved.
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.
To install OBO::Util::Set, copy and paste the appropriate command in to your terminal.
cpanm
cpanm OBO::Util::Set
CPAN shell
perl -MCPAN -e shell install OBO::Util::Set
For more information on module installation, please visit the detailed CPAN module installation guide.