Demonstration program for the Ensembl ontology database and API:

Fetching a GO term and then using it to get genes.

misc-scripts/ontology/scripts/demo1.pl

+#!/usr/bin/perl -w
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Registry;
+
+my $registry = 'Bio::EnsEMBL::Registry';
+
+$registry->load_registry_from_db(
+  '-host' => 'ensembldb.ensembl.org',
+  '-user' => 'anonymous'
+);
+
+my $accession = 'GO:0030326';
+
+# Get a GO term adaptor and a gene adaptor (for human).
+my $go_adaptor =
+  $registry->get_adaptor( 'Multi', 'Ontology', 'GOTerm' );
+
+my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
+
+# Fetch a GO term by its accession.
+my $term = $go_adaptor->fetch_by_accession($accession);
+
+# Use the GO term to get a bunch of genes cross-referenced to this GO
+# term or to any of its descendant terms.
+my @genes = @{ $gene_adaptor->fetch_all_by_GOTerm($term) };
+
+printf( "Genes associated with the term '%s' (%s):\n",
+  $term->accession(), $term->name() );
+
+foreach my $gene (@genes) {
+  printf( "stable ID = %s, external DB = %s, external name = %s\n",
+    $gene->stable_id(), $gene->external_db(), $gene->external_name() );
+}
+
+
+# $Id$