[ENSCORESW-477]. Added methods to allow lookup of OntologyTerm from an OntologyXref

modules/Bio/EnsEMBL/OntologyXref.pm

@@ -64,9 +64,40 @@ identifier but with different evidence tags.  For this reason a single
 package Bio::EnsEMBL::OntologyXref;
 
 use strict;
+use warnings;
 
 use base qw( Bio::EnsEMBL::DBEntry );
 
+require Bio::EnsEMBL::Registry;
+
+=head2 get_OntologyTerm
+
+  Example    : $ontology_xref->get_OntologyTerm();
+  Description: Queries the OntologyTermAdaptor for a term which is the same 
+               as the primary id of this object. This method requires a
+               OntologyDBAdaptor to be available in the Bio::EnsEMBL::Registry. 
+               If you have loaded data from an Ensembl release using
+               Bio::EnsEMBL::Registry->load_registry_from_db() then this should
+               work.
+  Returntype : Bio::EnsEMBL::OntologyTerm
+  Exceptions : None
+  Caller     : general
+  Status     : Experimantal
+
+=cut
+
+
+sub get_OntologyTerm {
+  my ($self) = @_;
+  my $dbas = Bio::EnsEMBL::Registry->get_all_DBAdaptors(-GROUP => 'ontology');
+  foreach my $ontology_dba (@{$dbas}) {
+    my $ota = $ontology_dba->get_OntologyTermAdaptor();
+    my $term = $ota->fetch_by_accession($self->primary_id());
+    return $term if $term;
+  }
+  return;
+}
+
 =head2 add_linkage_type
 
   Arg [1]    : string $value

modules/t/ontologyTerm.t

@@ -14,21 +14,21 @@ use Bio::EnsEMBL::Translation;
 use Bio::EnsEMBL::Gene;
 use Bio::EnsEMBL::DnaDnaAlignFeature;
 
-# switch on the debug prints
+# switch on the note prints
 our $verbose = 0;
 
-debug("Startup test");
+note("Startup test");
 ok(1);
 
 my $multi = Bio::EnsEMBL::Test::MultiTestDB->new('ontology');
 
 my $odb = $multi->get_DBAdaptor("ontology");
-debug("Ontology database instatiated");
+note("Ontology database instatiated");
 ok($odb);
 
 my $human = Bio::EnsEMBL::Test::MultiTestDB->new();
 my $db = $human->get_DBAdaptor("core");
-debug("Test database instatiated");
+note("Test database instatiated");
 ok($db);
 my $go_adaptor = $odb->get_OntologyTermAdaptor();
 
@@ -69,6 +69,16 @@ is(@{$go_roots}, 1, "Found go roots");
 my $efo_roots = $go_adaptor->fetch_all_roots('efo');
 is(@{$efo_roots}, 0, "Found no efo roots");
 
+#Now go back to the OntologyXref & see if we can do the reverse lookup
+{
+  my $go_db_links = $genes->[0]->get_all_DBLinks('GO');
+  foreach my $dbentry (@{$go_db_links}) {
+    my $term = $dbentry->get_OntologyTerm();
+    my $direct_term = $go_adaptor->fetch_by_accession($dbentry->primary_id());
+    is_deeply($term, $direct_term, 'Fetching the OntologyTerm from the OntologyXref should match the same object from OntologyTermAdaptor');
+  }
+}
+
 
 
 done_testing();