Erick Antezana > ONTO-PERL-1.42 > OBO::Core::RelationshipType

Download:
ONTO-PERL/ONTO-PERL-1.42.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  2
Open  0
View/Report Bugs
Source  

id

  Usage    - print $relationship_type->id()
  Returns  - the relationship type ID
  Args     - the relationship type ID
  Function - gets/sets an ID

is_anonymous

  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.

name

  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

alt_id

  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

def

  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

def_as_string

  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

namespace

  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

comment

  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

subset

  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

synonym_set

  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

synonym_as_string

  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

xref_set

  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

xref_set_as_string

  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

domain

  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

range

  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

inverse_of

  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

is_cyclic

  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.

is_reflexive

  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.

is_symmetric

  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.

is_anti_symmetric

  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.

is_transitive

  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.

is_metadata_tag

  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.

is_class_level

  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.

transitive_over

  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

holds_over_chain

  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

is_functional

  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

is_inverse_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

intersection_of

  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

union_of

  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

disjoint_from

  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

created_by

  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

creation_date

  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

modified_by

  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

modification_date

  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

is_obsolete

  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.

replaced_by

  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)

consider

  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

builtin

  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

equals

  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

NAME ^

OBO::Core::RelationshipType - A type of relationship type in an ontology.

SYNOPSIS ^

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();

}

DESCRIPTION ^

A type of relationship in the ontology.

AUTHOR ^

Erick Antezana, <erick.antezana -@- gmail.com>

COPYRIGHT AND LICENSE ^

Copyright (c) 2006-2014 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.

syntax highlighting: