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EASR / ONTO-PERL-1.39 / doc / example01.html 
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<title>Finding all the terms and relationships in a given ontology</title>
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<h2>Finding and getting elements (e.g. terms, relationships)</h2>
	
<ol>
	<li><a href="#1">Find all the terms in a given ontology.</a></li>
		
	<li><a href="#2">Find all the relationships in a given ontology.</a></li>
		
	<li><a href="#3">Find all the terms using a regular expression for the ID.</a></li>
		
	<li><a href="#4">Get a specific term by name.</a></li>
		
	<li><a href="#5">Get a specific term by ID.</a></li>

</ol>
	
<ol>
	<li> <b><a name="1">Find all the terms in a given ontology:</a></b>
		<pre>
		
			use OBO::Parser::OBOParser;
			
			my $my_parser = OBO::Parser::OBOParser->new();
			my $ontology = $my_parser->work("gene_ontology_edit.obo");
	
			my @my_terms = @{$ontology->get_terms()}; # get all the terms
			
			foreach my $t (@my_terms) {
				print "The name of the term is: ", $t->name(), ", and its ID is:", $t->id(), "\n";
			}
			
		</pre>
	</li>
	
	<li> <b><a name="2">Find all the relationships in a given ontology:</a></b>
		<pre>
		
			use OBO::Parser::OBOParser;
			
			my $my_parser = OBO::Parser::OBOParser->new();
			my $ontology = $my_parser->work("my_obo_ontology.obo");
			
			my @my_rels= @{$ontology->get_relationships()}; # get all the relationships
			
			foreach my $r (@my_rels) {
				print "The ID of the relationhip is: ", $r->id();
			}
			
		</pre>
	</li>

	<li> <b><a name="3">Find all the terms using a regular expression for the ID:</a></b>
		<pre>
		
			use OBO::Parser::OBOParser;
			
			my $my_parser = OBO::Parser::OBOParser->new();
			my $ontology = $my_parser->work("my_obo_ontology.obo");
			
			my @my_terms = @{$ontology->get_terms("APO:G.*")}; # get all the terms with such an ID
			
			foreach my $t (@my_terms) {
				print "The name of the term is: ", $t->name();
			}
			
		</pre>
	</li>
	
	<li> <b><a name="4">Get a specific term by name:</a></b>
		<pre>
		
			use OBO::Parser::OBOParser;
			
			my $my_parser = OBO::Parser::OBOParser->new();
			my $ontology = $my_parser->work("my_obo_ontology.obo");
			
			my $my_term = $ontology->get_term_by_name("protein"); # get the term by name
			
			print "The ID of my term is: ", $t->id();
			
		</pre>
	</li>

	<li> <b><a name="5">Get a specific term by ID:</a></b>
		<pre>
		
			use OBO::Parser::OBOParser;
			
			my $my_parser = OBO::Parser::OBOParser->new();
			my $ontology1 = $my_parser->work("go.obo");
			my $ontology2 = $my_parser->work("apo.obo");
			
			my $my_term1 = $ontology1->get_term_by_id("GO:00007049"); # get the term by ID
			my $my_term2 = $ontology2->get_term_by_id("APO:P0000056"); # get the term by ID
			
			print "\nThe name of the term1 is: ", $my_term1->name();
			print "\nThe name of the term2 is: ", $my_term2->name();
			
		</pre>
	</li>
	
</ol>
	
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