union

  Usage    - $ome->union($o1, $o2, ...)
  Returns  - an ontology (OBO::Core::Ontology) being the union of the parameters (ontologies)
  Args     - the ontologies (OBO::Core::Ontology) to be united
  Function - creates an ontology having the union of terms and relationships from the given ontologies
  Remark 1 - the IDspace's are collected and added to the result ontology
  Remark 2 - the union is made on the basis of the IDs
  Remark 3 - the default namespace is taken from the last ontology argument
  Remark 4 - the merging order is important while merging definitions: the one from the last ontology will be taken
  

intersection

  Usage    - $ome->intersection($o1, $o2)
  Return   - an ontology (OBO::Core::Ontology) holding the 'intersection' of $o1 and $o2
  Args     - the two ontologies (OBO::Core::Ontology) to be intersected 
  Function - finds the intersection ontology from $o1 and $o2. All the common terms by ID 
             are added to the resulting ontology. This method provides a way of comparing two
             ontologies. The resulting ontology gives hints about the missing and identical
             terms (comparison done by term ID). A closer analysis should be done to identify
             the differences
  Remark   - Performance issues with huge ontologies
  

transitive_closure

  Usage    - $ome->transitive_closure($o, @transitive_relationship_types)
  Return   - an ontology (OBO::Core::Ontology) with the transitive closure
  Args     - the ontology (OBO::Core::Ontology) to be expanded and 
                         optionally an array with the transitive relationship 
                         types (by default: 'is_a' and 'part_of') to be considered
  Function - expands all the transitive relationships (e.g. is_a, part_of) along the
                         hierarchy and generates a new ontology holding all possible paths
  Remark   - Performance issues with huge ontologies.
           - an experimental code is enabled (flag: $composition) based on http://www.geneontology.org/GO.ontology.relations.shtml
  

transitive_reduction

  Usage    - $ome->transitive_reduction($o, @transitive_relationship_types)
  Return   - an ontology (OBO::Core::Ontology) ensuring transitive reduction
  Args     - an ontology (OBO::Core::Ontology) on which the transitive reduction algorithm will be applied 
                         and optionally an array with the transitive relationship types (by default: 'is_a' and 'part_of') to be considered
  Function - reduces all the transitive relationships (e.g. is_a, part_of) along the
                         hierarchy and generates a new ontology holding the minimal paths (relationships)
  Remark   - Performance issues with huge ontologies.
  

NAME

OBO::Util::Ontolome - A set of ontologies. This module supports the management of a set of ontologies.

SYNOPSIS

use OBO::Util::Set;

use strict;

my $o1 = OBO::Core::Ontology->new();

my $o2 = OBO::Core::Ontology->new();

my $o3 = OBO::Core::Ontology->new();

my $ome1 = OBO::Util::Ontolome->new();

$ome1->add($o1);

$ome1->add_all($o2, $o3);

my $ome2 = OBO::Util::Ontolome->new();

$ome2->add_all($o1, $o2, $o3);

my $inter_o1_and_o2 = $ome1->intersection($o1, $o2);

my $union_o1_and_o2 = $ome1->union($o1, $o2);

my $o1_transitive_reduction = $ome1->transitive_reduction($o1);

my $o2_transitive_closure = $ome1->transitive_closure($o2);

DESCRIPTION

An Ontolome is a collection of ontologies that contains no duplicate ontology elements. More formally, an Ontolome contains no pair of ontologies $e1 and $e2 such that $e1->equals($e2). As implied by its name, this package models the set of ontologies.

AUTHOR

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

COPYRIGHT AND LICENSE

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.

cpanm OBO::Util::Set

perl -MCPAN -e shell
install OBO::Util::Set