<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/>
<title>Examples of using ONTO-PERL</title>
</head>
<body>
<h2>Examples of using <a href="http://search.cpan.org/~EASR/ONTO-PERL/">ONTO-PERL</a></h2>
<ul>
<li><a href="example01.html">Finding and getting elements (e.g. terms, relationships)</a>
<ol>
<li><a href="example01.html#1">Find all the terms in a given ontology.</a></li>
<li><a href="example01.html#2">Find all the relationships in a given ontology.</a></li>
<li><a href="example01.html#3">Find all the terms using a regular expression for the ID.</a></li>
<li><a href="example01.html#4">Get a specific term by name.</a></li>
<li><a href="example01.html#5">Get a specific term by ID.</a></li>
</ol>
</li>
<li><a href="example02.html">Getting children terms and/or descendant ones</a>
<ol>
<li><a href="example02.html#1">Get all the descendant terms of a given term.</a></li>
<li><a href="example02.html#2">Get only the child terms of a given term.</a></li>
</ol>
</li>
<li><a href="example03.html">Getting parent terms and/or ancestor ones</a>
<ol>
<li><a href="example03.html#1">Get all the ancestor terms of a given term.</a></li>
<li><a href="example03.html#2">Get the only the parent terms of a given term.</a></li>
</ol>
</li>
<li><a href="example04.html">Intersection of ontologies</a>
<ol>
<li><a href="example04.html#1">Find out the intersection of two given ontologies <i>o1</i> and <i>o3</i>.</a></li>
</ol>
</li>
<li><a href="example05.html">Getting a term by its features (e.g. synonyms, xref)</a>
<ol>
<li><a href="example05.html#1">Get a term by its name or any of its synonyms.</a></li>
<li><a href="example05.html#2">Get a term by one of its xref's.</a></li>
</ol>
</li>
<li><a href="example06.html">Working with obsolete terms</a>
<ol>
<li><a href="example06.html#1">Get all the obsolete terms in a given ontology.</a></li>
</ol>
</li>
<li><a href="example07.html">Basic metrics in an ontology</a>
<ol>
<li><a href="example07.html#1">Get the total number of terms and relationships in a given ontology.</a></li>
</ol>
</li>
<li><a href="example08.html">Union of ontologies</a>
<ol>
<li><a href="example08.html#1">Find out the union of two given ontologies <i>o1</i> and <i>o4</i>.</a></li>
</ol>
</li>
<li><a href="example09.html">Working with sub-ontologies</a>
<ol>
<li><a href="example09.html#1">Building an ontology from an existing sub-ontology.</a></li>
</ol>
</li>
<li><a href="example10.html">Ontology merging</a>
<ol>
<li><a href="example10.html#1">Simple merging of several and disjoint OBO ontologies from the same IDspace.</a></li>
</ol>
</li>
<li><a href="example11.html">Manipulating Ontology Terms</a>
<ol>
<li><a href="example11.html#1">Manipulating Ontology Terms (names, IDs, xref's, definitions, and so forth).</a></li>
</ol>
</li>
<li><a href="example12.html">Working with an Ontology</a>
<ol>
<li><a href="example12.html#1">Manipulating an Ontology.</a></li>
<li><a href="example12.html#2">Getting sub-ontologies from a given ontology.</a></li>
<li><a href="example12.html#3">Get paths from a given term A to a term B and/or from A to a set of given terms.</a></li>
</ol>
</li>
<li><a href="example13.html">Exporting ontologies into different formats</a>
<ol>
<li><a href="example13.html#1">Export a given ontology to OWL format (oboInOwl mapping).</a></li>
<li><a href="example13.html#2">Export a given ontology to GML format.</a></li>
<li><a href="example13.html#3">Export a given ontology to XML format.</a></li>
<li><a href="example13.html#4">Export a given ontology to DOT format.</a></li>
<li><a href="example13.html#5">Export a given ontology to OBO format (spec 1.2).</a></li>
<li><a href="example13.html#6">Export a given ontology to RDF format.</a></li>
</ol>
</li>
</ul>
<h2>More information:</h2>
ONTO-PERL: An API supporting the development and analysis of bio-ontologies
E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
</body>
</html>