NAME
OBO::Core::Ontology - An ontology holding terms and their relationships
SYNOPSIS
use OBO::Core::Ontology;
use OBO::Core::Term;
use OBO::Core::Relationship;
use OBO::Core::RelationshipType;
use strict;
# three new terms
my $n1 = OBO::Core::Term->new();
my $n2 = OBO::Core::Term->new();
my $n3 = OBO::Core::Term->new();
# new ontology
my $onto = OBO::Core::Ontology->new;
$n1->id("CCO:P0000001");
$n2->id("CCO:P0000002");
$n3->id("CCO:P0000003");
$n1->name("One");
$n2->name("Two");
$n3->name("Three");
my $def1 = OBO::Core::Def->new();
$def1->text("Definition of One");
my $def2 = OBO::Core::Def->new();
$def2->text("Definition of Two");
my $def3 = OBO::Core::Def->new();
$def3->text("Definition of Three");
$n1->def($def1);
$n2->def($def2);
$n3->def($def3);
$onto->add_term($n1);
$onto->add_term($n2);
$onto->add_term($n3);
$onto->delete_term($n1);
$onto->add_term($n1);
# new term
my $n4 = OBO::Core::Term->new();
$n4->id("CCO:P0000004");
$n4->name("Four");
my $def4 = OBO::Core::Def->new();
$def4->text("Definition of Four");
$n4->def($def4);
$onto->delete_term($n4);
$onto->add_term($n4);
# add term as string
my $new_term = $onto->add_term_as_string("CCO:P0000005", "Five");
$new_term->def_as_string("This is a dummy definition", "[CCO:vm, CCO:ls, CCO:ea \"Erick Antezana\"]");
my $n5 = $new_term;
# five new relationships
my $r12 = OBO::Core::Relationship->new();
my $r23 = OBO::Core::Relationship->new();
my $r13 = OBO::Core::Relationship->new();
my $r14 = OBO::Core::Relationship->new();
my $r35 = OBO::Core::Relationship->new();
$r12->id("CCO:P0000001_is_a_CCO:P0000002");
$r23->id("CCO:P0000002_part_of_CCO:P0000003");
$r13->id("CCO:P0000001_participates_in_CCO:P0000003");
$r14->id("CCO:P0000001_participates_in_CCO:P0000004");
$r35->id("CCO:P0000003_part_of_CCO:P0000005");
$r12->type("is_a");
$r23->type("part_of");
$r13->type("participates_in");
$r14->type("participates_in");
$r35->type("part_of");
$r12->link($n1, $n2);
$r23->link($n2, $n3);
$r13->link($n1, $n3);
$r14->link($n1, $n4);
$r35->link($n3, $n5);
# get all terms
my $c = 0;
my %h;
foreach my $t (@{$onto->get_terms()}) {
$h{$t->id()} = $t;
$c++;}
# get terms with argument
my @processes = sort {$a->id() cmp $b->id()} @{$onto->get_terms("CCO:P.*")};
my @odd_processes = sort {$a->id() cmp $b->id()} @{$onto->get_terms("CCO:P000000[35]")};
$onto->idspace_as_string("CCO", "http://www.cellcycle.org/ontology/CCO");
my @same_processes = @{$onto->get_terms_by_subnamespace("P")};
my @no_processes = @{$onto->get_terms_by_subnamespace("p")};
# add relationships
$onto->add_relationship($r12);
$onto->add_relationship($r23);
$onto->add_relationship($r13);
$onto->add_relationship($r14);
$onto->add_relationship($r35);
# add relationships and terms linked by this relationship
my $n11 = OBO::Core::Term->new();
my $n21 = OBO::Core::Term->new();
$n11->id("CCO:P0000011"); $n11->name("One one"); $n11->def_as_string("Definition One one", "");
$n21->id("CCO:P0000021"); $n21->name("Two one"); $n21->def_as_string("Definition Two one", "");
my $r11_21 = OBO::Core::Relationship->new();
$r11_21->id("CCO:R0001121"); $r11_21->type("r11-21");
$r11_21->link($n11, $n21);
$onto->add_relationship($r11_21); # adds to the ontology the terms linked by this relationship
# get all relationships
my %hr;
foreach my $r (@{$onto->get_relationships()}) {
$hr{$r->id()} = $r;}
# get children
my @children = @{$onto->get_child_terms($n1)};
@children = @{$onto->get_child_terms($n3)};
my %ct;
foreach my $child (@children) {
$ct{$child->id()} = $child;}
@children = @{$onto->get_child_terms($n2)};
# get parents
my @parents = @{$onto->get_parent_terms($n3)};
@parents = @{$onto->get_parent_terms($n1)};
@parents = @{$onto->get_parent_terms($n2)};
# get all descendents
my @descendents1 = @{$onto->get_descendent_terms($n1)};
my @descendents2 = @{$onto->get_descendent_terms($n2)};
my @descendents3 = @{$onto->get_descendent_terms($n3)};
my @descendents5 = @{$onto->get_descendent_terms($n5)};
# get all ancestors
my @ancestors1 = @{$onto->get_ancestor_terms($n1)};
my @ancestors2 = @{$onto->get_ancestor_terms($n2)};
my @ancestors3 = @{$onto->get_ancestor_terms($n3)};
# get descendents by term subnamespace
my @descendents4 = @{$onto->get_descendent_terms_by_subnamespace($n1, 'P')};
my @descendents5 = @{$onto->get_descendent_terms_by_subnamespace($n2, 'P')};
my @descendents6 = @{$onto->get_descendent_terms_by_subnamespace($n3, 'P')};
my @descendents6 = @{$onto->get_descendent_terms_by_subnamespace($n3, 'R')};
# get ancestors by term subnamespace
my @ancestors4 = @{$onto->get_ancestor_terms_by_subnamespace($n1, 'P')};
my @ancestors5 = @{$onto->get_ancestor_terms_by_subnamespace($n2, 'P')};
my @ancestors6 = @{$onto->get_ancestor_terms_by_subnamespace($n3, 'P')};
my @ancestors6 = @{$onto->get_ancestor_terms_by_subnamespace($n3, 'R')};
# 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");
# add relationship types
$onto->add_relationship_type($r1);
$onto->add_relationship_type($r2);
$onto->add_relationship_type($r3);
# get descendents or ancestors linked by a particular relationship type
my $rel_type1 = $onto->get_relationship_type_by_name("is_a");
my $rel_type2 = $onto->get_relationship_type_by_name("part_of");
my $rel_type3 = $onto->get_relationship_type_by_name("participates_in");
my @descendents7 = @{$onto->get_descendent_terms_by_relationship_type($n5, $rel_type1)};
@descendents7 = @{$onto->get_descendent_terms_by_relationship_type($n5, $rel_type2)};
@descendents7 = @{$onto->get_descendent_terms_by_relationship_type($n2, $rel_type1)};
@descendents7 = @{$onto->get_descendent_terms_by_relationship_type($n3, $rel_type3)};
my @ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n1, $rel_type1)};
@ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n1, $rel_type2)};
@ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n1, $rel_type3)};
@ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n2, $rel_type2)};
# add relationship type as string
my $relationship_type = $onto->add_relationship_type_as_string("CCO:R0000004", "has_participant");
# get relationship types
my @rt = @{$onto->get_relationship_types()};
my %rrt;
foreach my $relt (@rt) {
$rrt{$relt->name()} = $relt;}
my @rtbt = @{$onto->get_relationship_types_by_term($n1)};
my %rtbth;
foreach my $relt (@rtbt) {
$rtbth{$relt} = $relt;}
# get_head_by_relationship_type
my @heads_n1 = @{$onto->get_head_by_relationship_type($n1, $onto->get_relationship_type_by_name("participates_in"))};
my %hbrt;
foreach my $head (@heads_n1) {
$hbrt{$head->id()} = $head;}
DESCRIPTION
This module has several methods to work with Ontologies in OBO and OWL formats, such as the Cell Cycle Ontology (http://www.cellcycleontology.org). Basically, it is a directed acyclic graph (DAG) holding the terms (OBO::Core::Term) which in turn are linked by relationships (OBO::Core::Relationship). These relationships have an associated relationship type (OBO::Core::RelationshipType).
AUTHOR
Erick Antezana, <erant@psb.ugent.be>
COPYRIGHT AND LICENSE
Copyright (C) 2006, 2007 by erant
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.
id
Usage - print $ontology->id() or $ontology->id($id)
Returns - the ontology ID (string)
Args - the ontology ID (string)
Function - gets/sets the ontology IDname
Usage - print $ontology->name() or $ontology->name($name)
Returns - the name (string) of the ontology
Args - the name (string) of the ontology
Function - gets/sets the name of the ontologyimports
Usage - $onto->imports() or $onto->imports($id1, $id2, $id3, ...)
Returns - a set (OBO::Util::Set) with the imported id ontologies
Args - the ontology id(s) (string)
Function - gets/sets the id(s) of the ontologies that are imported by this onedate
Usage - print $ontology->date()
Returns - the current date (in dd:MM:yyyy HH:mm format) of the ontology
Args - the current date (in dd:MM:yyyy HH:mm format) of the ontology
Function - gets/sets the date of the ontologydefault_namespace
Usage - print $ontology->default_namespace() or $ontology->default_namespace("cellcycle_ontology")
Returns - the default namespace (string) of this ontology
Args - the default namespace (string) of this ontology
Function - gets/sets the default namespace of this ontologyidspace
Usage - print $ontology->idspace() or $ontology->idspace("CCO http://www.cellcycleontology.org/ontology/owl#")
Returns - the id space (OBO::Core::IDspace) of this ontology
Args - the id space (OBO::Core::IDspace) of this ontology
Function - gets/sets the idspace of this ontologyidspace_as_string
Usage - $ontology->idspace_as_string($local_id, $uri, $description)
Returns - the idspace as string (string). Empty string is returned if the IDspace was not defined
Args - the local idspace (string), the uri (string) and the description (string)
Function - gets/sets the idspace of this ontologydata_version
Usage - print $ontology->data_version()
Returns - the data version (string) of this ontology
Args - the data version (string) of this ontology
Function - gets/sets the data version of this ontologysaved_by
Usage - print $ontology->saved_by()
Returns - the username of the person (string) to last save this ontology
Args - the username of the person (string) to last save this ontology
Function - gets/sets the username of the person to last save this ontologyremark
Usage - print $ontology->remark()
Returns - the remark (string) of this ontology
Args - the remark (string) of this ontology
Function - gets/sets the remark of this ontologysubsets
Usage - $onto->subsets() or $onto->subsets($ss1, $ss2, $ss3, ...)
Returns - a set (OBO::Util::Set) with the subsets used in this ontology. A subset is a view over an ontology
Args - the subset(s) (string) used in this ontology
Function - gets/sets the subset(s) of this ontology
synonym_type_def_set
Usage - $onto->synonym_type_def_set() or $onto->synonym_type_def_set($st1, $st2, $st3, ...)
Returns - a set (OBO::Util::SynonymTypeDefSet) with the synonym type defintions used in this ontology. A synonym type is a description of a user-defined synonym type
Args - the synonym type defintion(s) (OBO::Core::SynonymTypeDef) used in this ontology
Function - gets/sets the synonym type definitions (s) of this ontology
add_term
Usage - $ontology->add_term($term)
Returns - the just added term (OBO::Core::Term)
Args - the term (OBO::Core::Term) to be added. The ID of the term to be added must have already been defined.
Function - adds a term to this ontologyadd_term_as_string
Usage - $ontology->add_term_as_string($term_id, $term_name)
Returns - the just added term (OBO::Core::Term)
Args - the term id (string) and the term name (string) of term to be added
Function - adds a term to this ontologyadd_relationship_type
Usage - $ontology->add_relationship_type($relationship_type)
Returns - the just added relationship type (OBO::Core::RelationshipType)
Args - the relationship type to be added (OBO::Core::RelationshipType). The ID of the relationship type to be added must have already been defined.
Function - adds a relationship type to this ontologyadd_relationship_type_as_string
Usage - $ontology->add_relationship_type_as_string($relationship_type_id, $relationship_type_name)
Returns - the just added relationship type (OBO::Core::RelationshipType)
Args - the relationship type id (string) and the relationship type name (string) of the relationship type to be added
Function - adds a relationship type to this ontologydelete_term
Usage - $ontology->delete_term($term)
Returns - none
Args - the term (OBO::Core::Term) to be deleted
Function - deletes a term from this ontologyhas_term
Usage - print $ontology->has_term($term)
Returns - true or false
Args - the term (OBO::Core::Term) to be tested
Function - checks if the given term belongs to this ontologyhas_term_id
Usage - print $ontology->has_term_id($term_id)
Returns - true or false
Args - the term id (string) to be tested
Function - checks if the given term id corresponds to a term held by this ontologyhas_relationship_type
Usage - print $ontology->has_relationship_type($relationship_type)
Returns - true or false
Args - the relationship type (OBO::Core::RelationshipType) to be tested
Function - checks if the given relationship type belongs to this ontologyhas_relationship_type_id
Usage - print $ontology->has_relationship_type_id($relationship_type_id)
Returns - true or false
Args - the relationship type id (string) to be tested
Function - checks if the given relationship type id corresponds to a relationship type held by this ontologyhas_relationship_id
Usage - print $ontology->has_relationship_id($rel_id)
Returns - true or false
Args - the relationship id (string) to be tested
Function - checks if the given relationship id corresponds to a relationship held by this ontologyequals
Usage - print $ontology->equals($another_ontology)
Returns - either 1 (true) or 0 (false)
Args - the ontology (OBO::Core::Ontology) to compare with
Function - tells whether this ontology is equal to the parameterget_terms
Usage - $ontology->get_terms() or $ontology->get_terms("CCO:I.*")
Returns - the terms held by this ontology as a reference to an array of OBO::Core::Term's
Args - none or the regular expression for filtering the terms by id's
Function - returns the terms held by this ontologyget_terms_by_subnamespace
Usage - $ontology->get_terms_by_subnamespace() or $ontology->get_terms_by_subnamespace("P")
Returns - the terms held by this ontology corresponding to the requested subnamespace as a reference to an array of OBO::Core::Term's
Args - none or the subnamespace: 'P', 'I', and so on.
Function - returns the terms held by this ontology corresponding to the requested subnamespaceget_relationships
Usage - $ontology->get_relationships()
Returns - the relationships held by this ontology as a reference to an array of OBO::Core::Relationship's
Args - none
Function - returns the relationships held by this ontologyget_relationship_types
Usage - $ontology->get_relationship_types()
Returns - a reference to an array with the relationship types (OBO::Core::RelationshipType) held by this ontology
Args - none
Function - returns the relationship types held by this ontologyget_relationships_by_source_term
Usage - $ontology->get_relationships_by_source_term($source_term)
Returns - a reference to an array with the relationship (OBO::Core::Relationship) connecting this term to its children
Args - the term (OBO::Core::Term) for which its relationships will be found out
Function - returns the relationships associated to the given source termget_relationships_by_target_term
Usage - $ontology->get_relationships_by_target_term($target_term)
Returns - a reference to an array with the relationship (OBO::Core::Relationship) connecting this term to its parents
Args - the term (OBO::Core::Term) for which its relationships will be found out
Function - returns the relationships associated to the given target termget_term_by_id
Usage - $ontology->get_term_by_id($id)
Returns - the term (OBO::Core::Term) associated to the given ID
Args - the term's ID (string)
Function - returns the term associated to the given IDset_term_id
Usage - $ontology->set_term_id($term, $new_id)
Returns - the term (OBO::Core::Term) with its new ID
Args - the term (OBO::Core::Term) and its new term's ID (string)
Function - sets a new term ID for the given term get_relationship_type_by_id
Usage - $ontology->get_relationship_type_by_id($id)
Returns - the relationship type (OBO::Core::RelationshipType) associated to the given id
Args - the relationship type's id (string)
Function - returns the relationship type associated to the given idget_term_by_name
Usage - $ontology->get_term_by_name($name)
Returns - the term (OBO::Core::Term) associated to the given name
Args - the term's name (string)
Function - returns the term associated to the given name
Remark - the argument (string) is case sensitiveget_term_by_name_or_synonym
Usage - $ontology->get_term_by_name_or_synonym($name)
Returns - the term (OBO::Core::Term) associated to the given name or *EXACT* synonym
Args - the term's name or synonym (string)
Function - returns the term associated to the given name or *EXACT* synonym
Remark - this function should be carefully used since among ontologies there may be homonyms at the level of the synonyms (e.g. genes)
Remark - the argument (string) is case sensitiveget_terms_by_name
Usage - $ontology->get_terms_by_name($name)
Returns - the term set (OBO::Util::TermSet) with all the terms (OBO::Core::Term) having $name in their names
Args - the term's name (string)
Function - returns the terms having $name in their names get_relationship_type_by_name
Usage - $ontology->get_relationship_type_by_name($name)
Returns - the relationship type (OBO::Core::RelationshipType) associated to the given name
Args - the relationship type's name (string)
Function - returns the relationship type associated to the given nameadd_relationship
Usage - $ontology->add_relationship($relationship)
Returns - none
Args - the relationship (OBO::Core::Relationship) to be added between two existing terms or two relationship types
Function - adds a relationship between either two terms or two relationship types. If the terms or relationship types bound by this relationship are not yet in the ontology, they will be addedget_relationship_by_id
Usage - print $ontology->get_relationship_by_id()
Returns - the relationship (OBO::Core::Relationship) associated to the given id
Args - the relationship id (string)
Function - returns the relationship associated to the given relationship idget_child_terms
Usage - $ontology->get_child_terms($term)
Returns - a reference to an array with the child terms (OBO::Core::Term) of the given term
Args - the term (OBO::Core::Term) for which the children will be found
Function - returns the child terms of the given termget_parent_terms
Usage - $ontology->get_parent_terms($term)
Returns - a reference to an array with the parent terms (OBO::Core::Term) of the given term
Args - the term (OBO::Core::Term) for which the parents will be found
Function - returns the parent terms of the given termget_head_by_relationship_type
Usage - $ontology->get_head_by_relationship_type($term, $relationship_type) or $ontology->get_head_by_relationship_type($rel_type, $relationship_type)
Returns - a reference to an array of terms (OBO::Core::Term) or relationship types (OBO::Core::RelationshipType) pointed out by the relationship of the given type; otherwise undef
Args - the term (OBO::Core::Term) or relationship type (OBO::Core::RelationshipType) and the pointing relationship type (OBO::Core::RelationshipType)
Function - returns the terms or relationship types pointed out by the relationship of the given typeget_tail_by_relationship_type
Usage - $ontology->get_tail_by_relationship_type($term, $relationship_type) or $ontology->get_tail_by_relationship_type($rel_type, $relationship_type)
Returns - a reference to an array of terms (OBO::Core::Term) or relationship types (OBO::Core::RelationshipType) pointing out the given term by means of the given relationship type; otherwise undef
Args - the term (OBO::Core::Term) or relationship type (OBO::Core::RelationshipType) and the relationship type (OBO::Core::RelationshipType)
Function - returns the terms or relationship types pointing out the given term by means of the given relationship typeget_number_of_terms
Usage - $ontology->get_number_of_terms()
Returns - the number of terms held by this ontology
Args - none
Function - returns the number of terms held by this ontologyget_number_of_relationships
Usage - $ontology->get_number_of_relationships()
Returns - the number of relationships held by this ontology
Args - none
Function - returns the number of relationships held by this ontologyget_number_of_relationship_types
Usage - $ontology->get_number_of_relationship_types()
Returns - the number of relationship types held by this ontology
Args - none
Function - returns the number of relationship types held by this ontologyexport
Usage - $ontology->export($file_handle, $export_format)
Returns - exports this ontology
Args - the file handle (STDOUT, STDERR, ...) and the format: obo (by default), xml, owl, dot, gml, xgmml, sbml. Default file handle: STDOUT.
Function - exports this ontologysubontology_by_terms
Usage - $ontology->subontology_by_terms($term_set)
Returns - a subontology with the given terms from this ontology
Args - the terms (OBO::Util::TermSet) that will be included in the subontology
Function - creates a subontology based on the given terms from this ontologyget_subontology_from
Usage - $ontology->get_subontology_from($new_root_term)
Returns - a subontology from the given term of this ontology
Args - the term (OBO::Core::Term) that is the root of the subontology
Function - creates a subontology having as root the given termobo_id2owl_id
Usage - $ontology->obo_id2owl_id($term)
Returns - the ID for OWL representation.
Args - the OBO-type ID.
Function - Transform an OBO-type ID into an OWL-type one. E.g. CCO:I1234567 -> CCO_I1234567owl_id2obo_id
Usage - $ontology->owl_id2obo_id($term)
Returns - the ID for OBO representation.
Args - the OWL-type ID.
Function - Transform an OWL-type ID into an OBO-type one. E.g. CCO_I1234567 -> CCO:I1234567char_hex_http
Usage - $ontology->char_hex_http($seq)
Returns - the sequence with the hexadecimal representation for the http special characters
Args - the sequence of characters
Function - Transforms a http character to its equivalent one in hexadecimal. E.g. : -> %3Aget_descendent_terms
Usage - $ontology->get_descendent_terms($term)
Returns - a set with the descendent terms (OBO::Core::Term) of the given term
Args - the term (OBO::Core::Term) for which all the descendent will be found
Function - returns recursively all the child terms of the given termget_ancestor_terms
Usage - $ontology->get_ancestor_terms($term)
Returns - a set with the ancestor terms (OBO::Core::Term) of the given term
Args - the term (OBO::Core::Term) for which all the ancestors will be found
Function - returns recursively all the parent terms of the given termget_descendent_terms_by_subnamespace
Usage - $ontology->get_descendent_terms_by_subnamespace($term, subnamespace)
Returns - a set with the descendent terms (OBO::Core::Term) of the given subnamespace
Args - the term (OBO::Core::Term), the subnamespace (string, e.g. 'P', 'R' etc)
Function - returns recursively the given term's children of the given subnamespaceget_ancestor_terms_by_subnamespace
Usage - $ontology->get_ancestor_terms_by_subnamespace($term, subnamespace)
Returns - a set with the ancestor terms (OBO::Core::Term) of the given subnamespace
Args - the term (OBO::Core::Term), the subnamespace (string, e.g. 'P', 'R' etc)
Function - returns recursively the given term's parents of the given subnamespaceget_descendent_terms_by_relationship_type
Usage - $ontology->get_descendent_terms_by_relationship_type($term, $rel_type)
Returns - a set with the descendent terms (OBO::Core::Term) of the given term linked by the given relationship type
Args - OBO::Core::Term object, OBO::Core::RelationshipType object
Function - returns recursively all the child terms of the given term linked by the given relationship typeget_ancestor_terms_by_relationship_type
Usage - $ontology->get_ancestor_terms_by_relationship_type($term, $rel_type)
Returns - a set with the ancestor terms (OBO::Core::Term) of the given term linked by the given relationship type
Args - OBO::Core::Term object, OBO::Core::RelationshipType object
Function - returns recursively the parent terms of the given term linked by the given relationship typecreate_rel
Usage - $ontology->create_rel->($tail, $type, $head)
Returns - OBO::Core::Ontology object
Args - OBO::Core::(Term|Relationship) object, relationship type string, and the OBO::Core::(Term|Relationship) object,
Function - creates and adds to the ontology a new relationshipget_term_by_xref
Usage - $ontology->get_term_by_xref($db, $acc)
Returns - the term (OBO::Core::Term) associated with the given external database ID. 'undef' is returned if there is no term for the given arguments.
Args - the name of the external database and the ID (strings)
Function - returns the term associated with the given external database IDget_paths_term1_term2
Usage - $ontology->get_paths_term1_term2($term1, $term2)
Returns - an array of references to the paths between term1 and term2
Args - the IDs of the terms for which a path (or paths) will be found
Function - returns the path(s) linking term1 and terms2, where term1 is more specific than term2get_paths_term_terms
Usage - $ontology->get_paths_term_terms($term, $set_of_terms)
Returns - an array of references to the paths between a given term ID and a given set of terms IDs
Args - the IDs of the terms for which a path (or paths) will be found
Function - returns the path(s) linking term and the given set of terms