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EASR / ONTO-PERL-1.10 / doc / example01.html 

            

              
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<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/>
<title>Finding all the terms and relationships in a given ontology</title>
</head>
<body>
         
<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("my_obo_ontology.obo");
                         
                        my @my_terms = $ontology->@{$onto->get_terms()}; # get all the terms
                         
                        foreach my $t (@my_terms) {
                                print "The name of the term is: ", $t->name();
                        }
                         
                </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("CCO: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("cco.obo");
                         
                        my $my_term1 = $ontology1->get_term_by_id("GO:00007049"); # get the term by ID
                        my $my_term2 = $ontology2->get_term_by_id("CCO: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>
         
</body>
</html>