id

Usage    - print $term->id() or $term->id($id) 
Returns  - the term ID (string)
Args     - the term ID (string)
Function - gets/sets the ID of this term

idspace

Usage    - print $term->idspace() 
Returns  - the idspace of this term; otherwise, 'NN'
Args     - none
Function - gets the idspace of this term # TODO Does this method still makes sense?

subnamespace

Usage    - print $term->subnamespace() 
Returns  - the subnamespace of this term (character); otherwise, 'X'
Args     - none
Function - gets the subnamespace of this term

code

Usage    - print $term->code() 
Returns  - the code of this term (character); otherwise, '0000000'
Args     - none
Function - gets the code of this term

name

Usage    - print $term->name() or $term->name($name)
Returns  - the name (string) of this term
Args     - the name (string) of this term
Function - gets/sets the name of this term

is_anonymous

Usage    - print $term->is_anonymous() or $term->is_anonymous("1")
Returns  - either 1 (true) or 0 (false)
Args     - either 1 (true) or 0 (false)
Function - tells whether this term is anonymous or not.

alt_id

Usage    - $term->alt_id() or $term->alt_id($id1, $id2, $id3, ...)
Returns  - a set (OBO::Util::Set) with the alternate id(s) of this term
Args     - the alternate id(s) (string) of this term
Function - gets/sets the alternate id(s) of this term

def

Usage    - $term->def() or $term->def($def)
Returns  - the definition (OBO::Core::Def) of this term
Args     - the definition (OBO::Core::Def) of this term
Function - gets/sets the definition of the term

def_as_string

Usage    - $term->def_as_string() or $term->def_as_string("During meiosis, the synthesis of DNA proceeding from the broken 3' single-strand DNA end that uses the homologous intact duplex as the template.", "[GOC:elh, PMID:9334324]")
Returns  - the definition (string) of this term
Args     - the definition (string) of this term plus the dbxref list (string) describing the source of this definition
Function - gets/sets the definition of this term

namespace

Usage    - $term->namespace() or $term->namespace($ns1, $ns2, $ns3, ...)
Returns  - an array with the namespace(s) to which this term belongs
Args     - the namespace(s) to which this term belongs
Function - gets/sets the namespace(s) to which this term belongs

comment

Usage    - print $term->comment() or $term->comment("This is a comment")
Returns  - the comment (string) of this term
Args     - the comment (string) of this term
Function - gets/sets the comment of this term

subset

Usage    - $term->subset() or $term->subset($ss_name1, $ss_name2, $ss_name3, ...)
Returns  - an array with the subset name(s) to which this term belongs
Args     - the subset name(s) (string) to which this term belongs
Function - gets/sets the subset name(s) to which this term belongs

synonym_set

Usage    - $term->synonym_set() or $term->synonym_set($synonym1, $synonym2, $synonym3, ...)
Returns  - an array with the synonym(s) of this term
Args     - the synonym(s) (OBO::Core::Synonym) of this term
Function - gets/sets the synonym(s) of this term

synonym_as_string

Usage    - print $term->synonym_as_string() or $term->synonym_as_string('this is a synonym text', '[CCO:ea]', 'EXACT', 'UK_SPELLING')
Returns  - an array with the synonym(s) of this term
Args     - the synonym text (string), the dbxrefs (string), synonym scope (string) of this term, and optionally the synonym type name (string)
Function - gets/sets the synonym(s) of this term

xref_set

Usage    - $term->xref_set() or $term->xref_set($dbxref_set)
Returns  - a Dbxref set (OBO::Util::DbxrefSet) with the analogous xref(s) of this term in another vocabulary
Args     - a set of analogous xref(s) (OBO::Util::DbxrefSet) of this term in another vocabulary
Function - gets/sets the analogous xref(s) set of this term in another vocabulary

xref_set_as_string

Usage    - $term->xref_set_as_string() or $term->xref_set_as_string("[Reactome:20610, EC:2.3.2.12]")
Returns  - the dbxref set with the analogous xref(s) of this term; [] if the set is empty
Args     - the dbxref set with the analogous xref(s) of this term
Function - gets/sets the dbxref set with the analogous xref(s) of this term

intersection_of

Usage    - $term->intersection_of() or $term->intersection_of($t1, $t2, $r1, ...)
Returns  - an array with the terms/relations which define this term
Args     - a set (strings) of terms/relations which define this term
Function - gets/sets the set of terms/relatonships defining this term

union_of

Usage    - $term->union_of() or $term->union_of($t1, $t2, $r1, ...)
Returns  - an array with the terms/relations which define this term
Args     - a set (strings) of terms/relations which define this term
Function - gets/sets the set of terms/relatonships defining this term

disjoint_from

Usage    - $term->disjoint_from() or $term->disjoint_from($disjoint_term_id1, $disjoint_term_id2, $disjoint_term_id3, ...)
Returns  - the disjoint term id(s) (string(s)) from this one
Args     - the term id(s) (string) that is (are) disjoint from this one
Function - gets/sets the disjoint term(s) from this one

created_by

Usage    - print $term->created_by() or $term->created_by("erick_antezana")
Returns  - name (string) of the creator of the term, may be a short username, initials or ID
Args     - name (string) of the creator of the term, may be a short username, initials or ID
Function - gets/sets the name of the creator of the term

creation_date

Usage    - print $term->creation_date() or $term->creation_date("2010-04-13T01:32:36Z")
Returns  - date (string) of creation of the term specified in ISO 8601 format
Args     - date (string) of creation of the term specified in ISO 8601 format
Function - gets/sets the date of creation of the term

modified_by

Usage    - print $term->modified_by() or $term->modified_by("erick_antezana")
Returns  - name (string) of the modificator of the term, may be a short username, initials or ID
Args     - name (string) of the modificator of the term, may be a short username, initials or ID
Function - gets/sets the name of the modificator of the term

modification_date

Usage    - print $term->modification_date() or $term->modification_date("2010-04-13T01:32:36Z")
Returns  - date (string) of modification of the term specified in ISO 8601 format
Args     - date (string) of modification of the term specified in ISO 8601 format
Function - gets/sets the date of modification of the term

is_obsolete

Usage    - print $term->is_obsolete()
Returns  - either 1 (true) or 0 (false)
Args     - either 1 (true) or 0 (false)
Function - tells whether the term is obsolete or not. 'false' by default.

replaced_by

Usage    - $term->replaced_by() or $term->replaced_by($id1, $id2, $id3, ...)
Returns  - a set (OBO::Util::Set) with the id(s) of the replacing term(s)
Args     - the the id(s) of the replacing term(s) (string)
Function - gets/sets the the id(s) of the replacing term(s)

consider

Usage    - $term->consider() or $term->consider($id1, $id2, $id3, ...)
Returns  - a set (OBO::Util::Set) with the appropiate substitute(s) for an obsolete term
Args     - the appropiate substitute(s) for an obsolete term (string)
Function - gets/sets the appropiate substitute(s) for this obsolete term

builtin

Usage    - $term->builtin() or $term->builtin(1) or $term->builtin(0)
Returns  - tells if this term is builtin to the OBO format; false by default
Args     - 1 (true) or 0 (false)
Function - gets/sets the value indicating whether this term is builtin to the OBO format

equals

Usage    - print $term->equals($another_term)
Returns  - either 1 (true) or 0 (false)
Args     - the term (OBO::Core::Term) to compare with
Function - tells whether this term is equal to the parameter

NAME

OBO::Core::Term - A universal/term/class/concept in an ontology.

SYNOPSIS

use OBO::Core::Term;

use OBO::Core::Def;

use OBO::Util::DbxrefSet;

use OBO::Core::Dbxref;

use OBO::Core::Synonym;

use strict;

# three new terms

my $n1 = OBO::Core::Term->new();

my $n2 = OBO::Core::Term->new();

my $n3 = OBO::Core::Term->new();

# id's

$n1->id("CCO:P0000001");

$n2->id("CCO:P0000002");

$n3->id("CCO:P0000003");

# alt_id

$n1->alt_id("CCO:P0000001_alt_id");

$n2->alt_id("CCO:P0000002_alt_id1", "CCO:P0000002_alt_id2", "CCO:P0000002_alt_id3", "CCO:P0000002_alt_id4");

# name

$n1->name("One");

$n2->name("Two");

$n3->name("Three");

$n1->is_obsolete(1);

$n1->is_obsolete(0);

$n1->is_anonymous(1);

$n1->is_anonymous(0);

# synonyms

my $syn1 = OBO::Core::Synonym->new();

$syn1->scope('EXACT');

my $def1 = OBO::Core::Def->new();

$def1->text("Hola mundo1");

my $sref1 = OBO::Core::Dbxref->new();

$sref1->name("CCO:vm");

my $srefs_set1 = OBO::Util::DbxrefSet->new();

$srefs_set1->add($sref1);

$def1->dbxref_set($srefs_set1);

$syn1->def($def1);

$n1->synonym($syn1);

my $syn2 = OBO::Core::Synonym->new();

$syn2->scope('BROAD');

my $def2 = OBO::Core::Def->new();

$def2->text("Hola mundo2");

my $sref2 = OBO::Core::Dbxref->new();

$sref2->name("CCO:ls");

$srefs_set1->add_all($sref1);

my $srefs_set2 = OBO::Util::DbxrefSet->new();

$srefs_set2->add_all($sref1, $sref2);

$def2->dbxref_set($srefs_set2);

$syn2->def($def2);

$n2->synonym($syn2);

my $syn3 = OBO::Core::Synonym->new();

$syn3->scope('BROAD');

my $def3 = OBO::Core::Def->new();

$def3->text("Hola mundo2");

my $sref3 = OBO::Core::Dbxref->new();

$sref3->name("CCO:ls");

my $srefs_set3 = OBO::Util::DbxrefSet->new();

$srefs_set3->add_all($sref1, $sref2);

$def3->dbxref_set($srefs_set3);

$syn3->def($def3);

$n3->synonym($syn3);

# synonym as string

$n2->synonym_as_string("Hello world2", "[CCO:vm2, CCO:ls2]", "EXACT");

# creator + date

$n1->created_by("erick_antezana");

$n1->creation_date("2009-04-13T01:32:36Z ");

# xref

$n1->xref("Uno");

$n1->xref("Eins");

$n1->xref("Een");

$n1->xref("Un");

$n1->xref("Uj");

my $xref_length = $n1->xref()->size();

my $def = OBO::Core::Def->new();

$def->text("Hola mundo");

my $ref1 = OBO::Core::Dbxref->new();

my $ref2 = OBO::Core::Dbxref->new();

my $ref3 = OBO::Core::Dbxref->new();

$ref1->name("CCO:vm");

$ref2->name("CCO:ls");

$ref3->name("CCO:ea");

my $refs_set = OBO::Util::DbxrefSet->new();

$refs_set->add_all($ref1,$ref2,$ref3);

$def->dbxref_set($refs_set);

$n1->def($def);

$n2->def($def);

# def as string

$n2->def_as_string("This is a dummy definition", '[CCO:vm, CCO:ls, CCO:ea "Erick Antezana"] {opt=first}');

my @refs_n2 = $n2->def()->dbxref_set()->get_set();

my %r_n2;

foreach my $ref_n2 (@refs_n2) {

$r_n2{$ref_n2->name()} = $ref_n2->name();

}

DESCRIPTION

A Term in the ontology. c.f. OBO flat file specification.

AUTHOR

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

COPYRIGHT AND LICENSE

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.

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