Manipulating an Ontology:
use OBO::Core::Ontology;
use OBO::Core::Term;
use OBO::Core::Relationship;
use OBO::Core::RelationshipType;
use OBO::Core::SynonymTypeDef;
use OBO::Parser::OBOParser;
use OBO::Util::TermSet;
# three new terms
my $n1 = OBO::Core::Term->new();
my $n2 = OBO::Core::Term->new();
my $n3 = OBO::Core::Term->new();
# new ontology
my $onto = OBO::Core::Ontology->new();
if ($onto->get_number_of_terms() == 0 && $onto->get_number_of_relationships()) {
# the ontology is empty !
# terms are added later...
}
$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 Tres");
$n1->def($def1);
$n2->def($def2);
$n3->def($def3);
$n1->xref_set_as_string("[GO:0000001]");
$n2->xref_set_as_string("[GO:0000002]");
$n3->xref_set_as_string("[GO:0000003]");
$onto->add_term($n1);
$onto->add_term($n2);
$onto->add_term($n3);
if ($onto->has_term($n1) && $onto->has_term($n2) && $onto->has_term($n3)) {
# should enter here
}
# modifying a term name directly
$n3->name("Trej");
# now: $onto->get_term_by_id("CCO:P0000003")->name() should be "Trej"
# modifying a term name via the ontology
$onto->get_term_by_id("CCO:P0000003")->name("Three");
# now: $onto->get_term_by_id("CCO:P0000003")->name() should be "Three"
# now: $onto->get_number_of_terms() should be 3
# now: $onto->get_number_of_relationships() should still be 0
$onto->delete_term($n1);
# now: $onto->has_term($n1) should be FALSE
# now: $onto->get_number_of_terms() should be 2
# now: $onto->get_number_of_relationships() should still be 0
$onto->add_term($n1);
# now: $onto->has_term($n1) should be 1
# now: $onto->get_number_of_terms() should be 3
# now: $onto->get_number_of_relationships() should be 0
# 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);
# now: $onto->has_term($n4) is FALSE
$onto->delete_term($n4);
# now: $onto->has_term($n4) is still FALSE
$onto->add_term($n4);
# now: $onto->has_term($n4) should be TRUE
# 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\"]");
# now: $onto->has_term($new_term) should be 1
# now: $onto->get_term_by_id("CCO:P0000005")->equals($new_term) should be TRUE
# now: $onto->get_number_of_terms() should be 5
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();
# setting up IDs
$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");
# setting up the relationship types
$r12->type("is_a");
$r23->type("part_of");
$r13->type("participates_in");
$r14->type("participates_in");
$r35->type("part_of");
# linking terms:
$r12->link($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;
# now: $onto->has_term_id("CCO:P0000003") should be TRUE
# now: $onto->has_term_id("CCO:P0000033") should be FALSE
foreach my $t (@{$onto->get_terms()}) {
if ($t->id() eq "CCO:P0000003"){
# now: $onto->has_term($t) should be TRUE
$onto->set_term_id($t, "CCO:P0000033");
# now: $onto->has_term($t) should be TRUE
$t = $onto->get_term_by_id("CCO:P0000033");
}
$t->name("Uj") if ($t->id() eq "CCO:P0000001");
$h{$t->id()} = $t;
$c++;
}
# now: $onto->has_term_id("CCO:P0000003") should be FALSE
# $onto->has_term_id("CCO:P0000033") should be TRUE
# now: $onto->get_number_of_terms() should be 5
# now: $c should be 5
# now: $h{"CCO:P0000001"}->name() eq "Uj" should be TRUE since the name has been changed above
# now: $h{"CCO:P0000002"}->name() eq "Two" should be TRUE
# now: $h{"CCO:P0000033"}->name() eq "Three" should be TRUE since the ID has been changed above
# now: $h{"CCO:P0000004"}->name() eq "Four" should be TRUE
# now: $h{"CCO:P0000005"}->name() eq "Five" should be TRUE
# modifying a term ID via the ontology
# now: $onto->set_term_id($onto->get_term_by_id("CCO:P0000033"), "CCO:P0000003")->id() eq "CCO:P0000003" should be TRUE
# now: $onto->has_term_id("CCO:P0000003") should be TRUE
# now: $onto->has_term_id("CCO:P0000033") should be FALSE
# now: $onto->get_number_of_terms() should be 5
# get terms with argument
my @processes = sort {$a->id() cmp $b->id()} @{$onto->get_terms("CCO:P.*")};
# now: @processes should have 5 elements
my @odd_processes = sort {$a->id() cmp $b->id()} @{$onto->get_terms("CCO:P000000[35]")};
# now: @odd_processes should have 1 element
# now: $odd_processes[0]->id() eq "CCO:P0000003" should be TRUE
# now: $odd_processes[1]->id() eq "CCO:P0000005" should be TRUE
# now: $onto->idspace_as_string() eq "" should be TRUE
$onto->idspace_as_string("CCO", "http://www.cellcycle.org/ontology/CCO", "cell cycle ontology terms");
# now: $onto->idspace()->local_idspace() eq "CCO" should be TRUE
my @same_processes = @{$onto->get_terms_by_subnamespace("P")};
# now: @same_processes should be identical to @processes
my @no_processes = @{$onto->get_terms_by_subnamespace("p")};
# now: @no_processes should be empty
# get terms
# now: $onto->get_term_by_id("CCO:P0000001")->name() eq "Uj" should be TRUE
# now: $onto->get_term_by_name("Uj")->equals($n1) should be TRUE
$n1->synonym_as_string("Uno", "[CCO:ls, CCO:vm]", "EXACT");
# now: ($n1->synonym_as_string())[0] should be "Uno" [CCO:ls, CCO:vm]"
$n1->synonym_as_string("One", "[CCO:ls, CCO:vm]", "BROAD");
# now: $onto->get_term_by_name_or_synonym("Uno")->equals($n1) should be TRUE (needs to be EXACT)
# now: $onto->get_term_by_name_or_synonym("One") eq '' should be TRUE (undef due to BROAD)
# now: $onto->get_term_by_name("Two")->equals($n2) should be TRUE
# now: $onto->get_term_by_name("Three")->equals($n3) should be TRUE
# now: $onto->get_term_by_name("Four")->equals($n4) should be TRUE
# xref's
# now: $onto->get_term_by_xref("GO", "0000001")->equals($n1) should be TRUE
# now: $onto->get_term_by_xref("GO", "0000002")->equals($n2) should be TRUE
# now: $onto->get_term_by_xref("GO", "0000003")->equals($n3) should be TRUE
# contains
# now: $onto->get_terms_by_name("Uj")->contains($n1) should be TRUE
# now: $onto->get_terms_by_name("Two")->contains($n2) should be TRUE
# now: $onto->get_terms_by_name("Three")->contains($n3) should be TRUE
# now: $onto->get_terms_by_name("Four")->contains($n4) should be TRUE
# add relationships
$onto->add_relationship($r12);
# now: $onto->get_relationship_by_id("CCO:P0000001_is_a_CCO:P0000002")->head()->id() should be "CCO:P0000002"
# now: $onto->has_relationship_id("CCO:P0000001_is_a_CCO:P0000002") should be TRUE
my @relas = @{$onto->get_relationships_by_target_term($onto->get_term_by_id("CCO:P0000002"))};
# now: $relas[0]->id() should be "CCO:P0000001_is_a_CCO:P0000002"
# now: $relas[0]->tail()->id() should be "CCO:P0000001"
# now: $relas[0]->head()->id() should be "CCO:P0000002"
# add relationships
$onto->add_relationship($r23);
$onto->add_relationship($r13);
$onto->add_relationship($r14);
$onto->add_relationship($r35);
# now: $onto->get_number_of_terms() should be 5
# now: $onto->get_number_of_relationships() should be 5
# 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:L0001121"); $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
# now: $onto->get_number_of_terms() should be 7
# now: $onto->get_number_of_relationships() should be 6
# get all the relationships
my %hr;
foreach my $r (@{$onto->get_relationships()}) {
$hr{$r->id()} = $r;
}
# now: $hr{"CCO:P0000001_is_a_CCO:P0000002"}->head()->equals($n2) should be TRUE
# now: $hr{"CCO:P0000002_part_of_CCO:P0000003"}->head()->equals($n3) should be TRUE
# now: $hr{"CCO:P0000001_participates_in_CCO:P0000003"}->head()->equals($n3) should be TRUE
# now: $hr{"CCO:P0000001_participates_in_CCO:P0000004"}->head()->equals($n4) should be TRUE
# recover a previously stored relationship
# now: $onto->get_relationship_by_id("CCO:P0000001_participates_in_CCO:P0000003")->equals($r13) should be TRUE
# now: $onto->has_relationship_id("CCO:P0000001_participates_in_CCO:P0000003") should be TRUE
# get children
my @children = @{$onto->get_child_terms($n1)};
# now: @children should be 0
@children = @{$onto->get_child_terms($n3)};
# now: @children should have 1 element
my %ct;
foreach my $child (@children) {
$ct{$child->id()} = $child;
}
# now: $ct{"CCO:P0000002"}->equals($n2) should be TRUE
# now: $ct{"CCO:P0000001"}->equals($n1) should be TRUE
@children = @{$onto->get_child_terms($n2)};
# now: @children should have one element
# now: $children[0]->id should be "CCO:P0000001"
# get parents
my @parents = @{$onto->get_parent_terms($n3)};
# now: @parents should have 1 element
@parents = @{$onto->get_parent_terms($n1)};
# now: @parents should have 3 element
@parents = @{$onto->get_parent_terms($n2)};
# now: @parentsshould have 1 element
# now: $parents[0]->id should be "CCO:P0000003"
# get all descendents
my @descendents1 = @{$onto->get_descendent_terms($n1)};
# now: @descendents1 should have 0 elements
my @descendents2 = @{$onto->get_descendent_terms($n2)};
# now: @descendents2 should have 1 element
# now: $descendents2[0]->id should be "CCO:P0000001"
my @descendents3 = @{$onto->get_descendent_terms($n3)};
# now: @descendents3 should have 2 elements
my @descendents5 = @{$onto->get_descendent_terms($n5)};
# now: @descendents5 should have 3 elements
# get all ancestors
my @ancestors1 = @{$onto->get_ancestor_terms($n1)};
# now: @ancestors1 should have 4 elements
my @ancestors2 = @{$onto->get_ancestor_terms($n2)};
# now: @ancestors2) should have 2 elements
my @ancestors3 = @{$onto->get_ancestor_terms($n3)};
# now: @ancestors3) should have 1 element
# get descendents by term subnamespace
@descendents1 = @{$onto->get_descendent_terms_by_subnamespace($n1, 'P')};
# now: @descendents1 should have 0 elements
@descendents2 = @{$onto->get_descendent_terms_by_subnamespace($n2, 'P')};
# now: @descendents2 should have 1 element
# now: $descendents2[0]->id should be "CCO:P0000001"
@descendents3 = @{$onto->get_descendent_terms_by_subnamespace($n3, 'P')};
# now: @descendents3 should have 2 elements
@descendents3 = @{$onto->get_descendent_terms_by_subnamespace($n3, 'R')};
# now: @descendents3 should have 0 elements
# get ancestors by term subnamespace
@ancestors1 = @{$onto->get_ancestor_terms_by_subnamespace($n1, 'P')};
# now: @ancestors1) should have 4 elements
@ancestors2 = @{$onto->get_ancestor_terms_by_subnamespace($n2, 'P')};
# now: @ancestors2 should have 2 elements
@ancestors3 = @{$onto->get_ancestor_terms_by_subnamespace($n3, 'P')};
# now: @ancestors3 should have 1 element
@ancestors3 = @{$onto->get_ancestor_terms_by_subnamespace($n3, 'R')};
# now: @ancestors3) should have 0 elements
# three new relationships types
my $r1 = OBO::Core::RelationshipType->new();
my $r2 = OBO::Core::RelationshipType->new();
my $r3 = OBO::Core::RelationshipType->new();
$r1->id("is_a");
$r2->id("part_of");
$r3->id("participates_in");
$r1->name("is a");
$r2->name("part_of");
$r3->name("participates_in");
# add relationship types
$onto->add_relationship_type($r1);
# now: $onto->has_relationship_type($r1) should be TRUE
# now: $onto->has_relationship_type($onto->get_relationship_type_by_id("is_a")) should be TRUE
# now: $onto->has_relationship_type($onto->get_relationship_type_by_name("is a")) should be TRUE
# now: $onto->has_relationship_type_id("is_a") should be TRUE
$onto->add_relationship_type($r2);
# now: $onto->has_relationship_type($r2) should be TRUE
# now: $onto->has_relationship_type_id("part_of") should be TRUE
$onto->add_relationship_type($r3);
# now: $onto->has_relationship_type($r3) should be TRUE
# now: $onto->has_relationship_type_id("participates_in") should be TRUE
# now: $onto->get_number_of_relationship_types() should be 3
# 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, $rel_type1)};
# now: @descendents7 should have 0 element
@descendents7 = @{$onto->get_descendent_terms_by_relationship_type($n5, $rel_type2)};
# now: @descendents7 should have 2 elements
@descendents7 = @{$onto->get_descendent_terms_by_relationship_type($n2, $rel_type1)};
# now: @descendents7 should have 1 element
@descendents7 = @{$onto->get_descendent_terms_by_relationship_type($n3, $rel_type3)};
# now: @descendents7 should have 1 element
my @ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n1, $rel_type1)};
# now: @ancestors7 should have 1 element
@ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n1, $rel_type2)};
# now: @ancestors7 should have 0 elements
@ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n1, $rel_type3)};
# now: @ancestors7 should have 2 elements
@ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n2, $rel_type2)};
# now: @ancestors7 should have 2 elements
# add relationship type as string
my $relationship_type = $onto->add_relationship_type_as_string("has_participant", "has_participant");
# $onto->has_relationship_type($relationship_type) should be TRUE
# $onto->get_relationship_type_by_id("has_participant")->equals($relationship_type) should be TRUE
# $onto->get_number_of_relationship_types() should be 4
# get relationship types
my @rt = @{$onto->get_relationship_types()};
# now: @rt should have 4 elements
my %rrt;
foreach my $relt (@rt) {
$rrt{$relt->name()} = $relt;
}
# now: $rrt{"is a"}->name() should be "is a"
# now: $rrt{"part_of"}->name() should be "part_of"
# now: $rrt{"participates_in"}->name() should be "participates_in"
# now: $onto->get_relationship_type_by_id("is_a")->name() should be "is a"
# now: $onto->get_relationship_type_by_name("is a")->id() should be "is_a"
# now: $onto->get_relationship_type_by_name("part_of")->id() should be "part_of"
# now: $onto->get_relationship_type_by_name("participates_in")->id() should be "participates_in"
# get_relationships_by_(source|target)_term
my @rtbs = @{$onto->get_relationships_by_source_term($n1)};
my %rtbsh;
foreach my $rel (@rtbs) {
$rtbsh{$rel->type()} = $rel->type();
}
# now: $rtbsh{"participates_in"} should be "participates_in"
# now: $rtbsh{"is_a"} should be "is_a"
my @rtbt = @{$onto->get_relationships_by_target_term($n3)};
my %rtbth;
foreach my $rel (@rtbt) {
$rtbth{$rel->type()} = $rel->type();
}
# now: $rtbth{"participates_in"} should be "participates_in");
# now: $rtbth{"part_of"} should be "part_of");
# get_head_by_relationship_type
my @heads_n1 = @{$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;
}
# now: $hbrt{"CCO:P0000003"}->equals($n3) should be TRUE
# now: $hbrt{"CCO:P0000004"}->equals($n4) should be TRUE
# now: @{$onto->get_head_by_relationship_type($n1, $onto->get_relationship_type_by_name("is a"))}[0]->equals($n2) should be TRUE
# get_tail_by_relationship_type
# now: @{$onto->get_tail_by_relationship_type($n3, $onto->get_relationship_type_by_name("participates_in"))}[0]->equals($n1) should be TRUE
# now: @{$onto->get_tail_by_relationship_type($n2, $onto->get_relationship_type_by_name("is a"))}[0]->equals($n1) should be TRUE
# export
$onto->remarks("This is a test ontology");
$onto->export(\*STDOUT); # by default in OBO format (spec 1.2)
# subontology_by_terms
my $terms = OBO::Util::TermSet->new();
$terms->add_all($n1, $n2, $n3);
my $so = $onto->subontology_by_terms($terms);
# now: $so->get_number_of_terms() should be 3
# now: $so->has_term($n1) should be TRUE
# now: $so->has_term($n2) should be TRUE
# now: $so->has_term($n3) should be TRUE
$n1->name("mitotic cell cycle");
$n2->name("cell cycle process");
$n3->name("re-entry into mitotic cell cycle after pheromone arrest");
# now: $onto->get_term_by_name("mitotic cell cycle")->equals($n1) should be TRUE
# now: $onto->get_term_by_name("cell cycle process")->equals($n2) should be TRUE
# now: $onto->get_term_by_name("re-entry into mitotic cell cycle after pheromone arrest")->equals($n3) should be TRUE
# now: $onto->get_terms_by_name("mitotic cell cycle")->contains($n1) should be TRUE
# now: $onto->get_terms_by_name("cell cycle process")->contains($n2) should be TRUE
# now: $onto->get_terms_by_name("re-entry into mitotic cell cycle after pheromone arrest")->contains($n3) should be TRUE
# now: $onto->get_terms_by_name("mitotic cell cycle")->size() should be 2
# now: $onto->get_terms_by_name("mitotic cell cycle")->contains($n1) should be TRUE
# now: $onto->get_terms_by_name("mitotic cell cycle")->contains($n3) should be TRUE
# now: ($onto->get_terms_by_name("cell cycle process")->get_set())[0]->id() should be identical to $n2->id()
# now: ($onto->get_terms_by_name("re-entry into mitotic cell cycle after pheromone arrest")->get_set())[0]->id() should be identical to $n3->id()
# now: $onto->get_terms_by_name("cell cycle")->size() should be 3
$so->imports("o1", "02");
$so->date("11:03:2007 21:46");
$so->data_version("09:03:2007 19:30");
$so->idspace_as_string("CCO", "http://www.cellcycleontology.org/ontology/CCO", "cell cycle terms");
# now: $so->idspace->local_idspace() should be "CCO"
# now: $so->idspace->uri() should be "http://www.cellcycleontology.org/ontology/CCO"
# now: $so->idspace->description() should be "cell cycle terms"
$so->remarks("This is a test ontology");
$so->subsets("Jukumari Term used for jukumari", "Jukucha Term used for jukucha");
my $std1 = OBO::Core::SynonymTypeDef->new();
my $std2 = OBO::Core::SynonymTypeDef->new();
$std1->synonym_type_def_as_string("acronym", "acronym", "EXACT");
$std2->synonym_type_def_as_string("common_name", "common name", "EXACT");
$so->synonym_type_def_set($std1, $std2);
$n1->subset("Jukumari");
$n1->subset("Jukucha");
$n2->def_as_string("This is a dummy definition", "[CCO:vm, CCO:ls, CCO:ea \"Erick Antezana\"] {opt=first}");
$n1->xref_set_as_string("CCO:ea");
$n3->synonym_as_string("This is a dummy synonym definition", "[CCO:vm, CCO:ls, CCO:ea \"Erick Antezana\"] {opt=first}", "EXACT");
$n3->alt_id("CCO:P0000033");
$n3->namespace("cellcycle");
$n3->is_obsolete("1");
$n3->union_of("GO:0001");
$n3->union_of("GO:0002");
$n2->intersection_of("GO:0003");
$n2->intersection_of("part_of GO:0004");
# export the ontology to OWL
$so->export(\*STDERR, 'owl');
# export the ontology to OBO
$so->export(\*STDERR, 'obo');
# now: $onto->get_number_of_relationships() should be 6
$onto->create_rel($n4, 'part_of', $n5);
# now: $onto->get_number_of_relationships() should be 7
Get paths from a given term A to a term B and/or from A to a set of given terms:
# get paths from term1 to term2
my $o1 = OBO::Core::Ontology->new();
my $d5 = OBO::Core::Term->new();
my $d2 = OBO::Core::Term->new();
my $d6 = OBO::Core::Term->new();
my $d1 = OBO::Core::Term->new();
my $d7 = OBO::Core::Term->new();
my $d8 = OBO::Core::Term->new();
my $d10 = OBO::Core::Term->new();
my $d11 = OBO::Core::Term->new();
my $d20 = OBO::Core::Term->new();
my $d21 = OBO::Core::Term->new();
my $d32 = OBO::Core::Term->new();
my $d23 = OBO::Core::Term->new();
my $d24 = OBO::Core::Term->new();
my $d25 = OBO::Core::Term->new();
my $d26 = OBO::Core::Term->new();
my $d27 = OBO::Core::Term->new();
my $d28 = OBO::Core::Term->new();
my $d29 = OBO::Core::Term->new();
$d5->id("5");
$d2->id("2");
$d6->id("6");
$d1->id("1");
$d7->id("7");
$d8->id("8");
$d10->id("10");
$d11->id("11");
$d20->id("20");
$d21->id("21");
$d32->id("32");
$d23->id("23");
$d24->id("24");
$d25->id("25");
$d26->id("26");
$d27->id("27");
$d28->id("28");
$d29->id("29");
$d5->name("5");
$d2->name("2");
$d6->name("6");
$d1->name("1");
$d7->name("7");
$d8->name("8");
$d10->name("10");
$d11->name("11");
$d20->name("20");
$d21->name("21");
$d32->name("32");
$d23->name("23");
$d24->name("24");
$d25->name("25");
$d26->name("26");
$d27->name("27");
$d28->name("28");
$d29->name("29");
my $r = 'is_a';
$o1->add_relationship_type_as_string($r, $r);
$o1->create_rel($d5,$r,$d2);
$o1->create_rel($d2,$r,$d6);
$o1->create_rel($d2,$r,$d1);
$o1->create_rel($d2,$r,$d7);
$o1->create_rel($d7,$r,$d8);
$o1->create_rel($d7,$r,$d11);
$o1->create_rel($d1,$r,$d10);
$o1->create_rel($d1,$r,$d8);
$o1->create_rel($d5,$r,$d23);
$o1->create_rel($d11,$r,$d28);
$o1->create_rel($d28,$r,$d29);
$o1->create_rel($d8,$r,$d27);
$o1->create_rel($d27,$r,$d26);
$o1->create_rel($d10,$r,$d24);
$o1->create_rel($d24,$r,$d25);
$o1->create_rel($d25,$r,$d26);
$o1->create_rel($d6,$r,$d20);
$o1->create_rel($d20,$r,$d21);
$o1->create_rel($d20,$r,$d32);
$o1->create_rel($d21,$r,$d25);
# get paths from term1 to term2
my @ref_paths = $o1->get_paths_term1_term2($d5->id(), $d26->id());
# now: @ref_paths should have 4 elements
# get paths from term1 to term2
@ref_paths = $o1->get_paths_term1_term2($d5->id(), $d29->id());
# now: @ref_paths should have 1 element
my @p = ("5_is_a_2", "2_is_a_7", "7_is_a_11", "11_is_a_28", "28_is_a_29");
foreach my $ref_path (@ref_paths) {
foreach my $tt (@$ref_path) {
# now: $tt->id() shoudl be identical to shift @p
}
}
my $stop = OBO::Util::Set->new();
map {$stop->add($_->id())} @{$o1->get_terms()};
# get the paths from a given term to a given set of terms
my @pref1 = $o1->get_paths_term_terms($d5->id(), $stop);
# now: @pref1 should have 23 elements, i.e., 23 paths