OntoCAT Guide

• Quick Start
• ​JavaDoc (latest one always included with the distribution)

R code examples

• ​R Example 1 - Gene enrichment test and grouping of results
• ​R Example 2 - Search and re-annotation of free-text to ontology
• ​R Example 3 - Operations with relations

Java code examples

Core functionality

• ​Example 1 - Shows how to list all ontologies available through OLS
• ​Example 2 - Shows how to list all ontologies available through NCBO BioPortal
• ​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)
• ​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

• ​Example 8 - Shows how to search a subtree of an ontology
• ​Example 9 - Shows how to cross reference one ontology with another
• ​Example 10 - Shows how to list all classes from an ontology
• ​Example 11 - Shows how to extract UMLS CUIs through NCBO BioPortal
• ​Example 12 - Shows how to extract hierarchy information for a particular term in an ontology
• ​Example 13 - Shows how to get functional roots in EFO and build hierarchy
• ​Example 14 - Shows how to run regression testing (compare) on two versions of the same ontology
• ​Example 17 - Shows how to get term paths and term neighbourhood
• ​Example 18 - Shows how to work with namespaces for local ontologies

Reasoning

(see more info)

• ​Example 15 - Shows how to use inferred hierarchy and compute partonomy
• ​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 ​a new ticket or the ​mailing list.