= OntoCAT Guide =
 * [wiki:OntocatInstallation Quick Start]
 * [http://ontocat.sourceforge.net/doc/index.html JavaDoc] (latest one always included with the distribution)
= R code examples =

 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/R/Example1.R R Example 1] - Gene enrichment test and grouping of results
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/R/Example2.R R Example 2] - Search and re-annotation of free-text to ontology
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/R/Example3.R R Example 3] - Operations with relations
= Java code examples =
== Core functionality ==
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example1.java Example 1] - Shows how to list all ontologies available through OLS
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example2.java Example 2] - Shows how to list all ontologies available through NCBO !BioPortal
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example3.java Example 3] - Shows how to search an OWL ontology

== Instantiating a ''virtual'' service ==
 * Example 4 - Shows how to sort and rank searches (removed in 1.0)
 * Example 5 - Shows how to cache an ontology service (removed in 1.0)
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example6.java Example 6] - Shows how to combine multiple ontologies
 * Example 7 - Shows how to translate ontology to a different namespace (removed in 1.0)

== Additional use cases ==
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example8.java Example 8] - Shows how to search a subtree of an ontology
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example9.java Example 9] - Shows how to cross reference one ontology with another
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example10.java Example 10] - Shows how to list all classes from an ontology
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example11.java Example 11]  - Shows how to extract UMLS CUIs through NCBO !BioPortal
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example12.java Example 12] - Shows how to extract hierarchy information for a particular term in an ontology
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example13.java Example 13] - Shows how to get functional roots in EFO and build hierarchy 
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example14.java Example 14] - Shows how to run regression testing (compare) on two versions of the same ontology
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example17.java Example 17] - Shows how to get term paths and term neighbourhood
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example18.java Example 18] - Shows how to work with namespaces for local ontologies

== Reasoning ==
(see [wiki:Reasoning more info])
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example15.java Example 15] - Shows how to use inferred hierarchy and compute partonomy
 * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example16.java Example 16] - Shows how to compute all relationships across the whole ontology (parallelised by multiprocessing)

Not found an example you're interested in? Feel free to request it via [http://www.ontocat.org/newticket a new ticket] or the [https://lists.sourceforge.net/lists/listinfo/ontocat-users mailing list].