| | 1 | = OntoCAT Guide = |
| | 2 | * [wiki:OntocatInstallation Quick Start] |
| | 3 | * [http://ontocat.sourceforge.net/doc/index.html JavaDoc] (latest one always included with the distribution) |
| | 4 | = R code examples = |
| | 5 | |
| | 6 | * [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 |
| | 7 | * [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 |
| | 8 | * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/R/Example3.R R Example 3] - Operations with relations |
| | 9 | = Java code examples = |
| | 10 | == Core functionality == |
| | 11 | * [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 |
| | 12 | * [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 |
| | 13 | * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example3.java Example 3] - Shows how to search an OWL ontology |
| | 14 | |
| | 15 | == Instantiating a ''virtual'' service == |
| | 16 | * Example 4 - Shows how to sort and rank searches (removed in 1.0) |
| | 17 | * Example 5 - Shows how to cache an ontology service (removed in 1.0) |
| | 18 | * [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/Example6.java Example 6] - Shows how to combine multiple ontologies |
| | 19 | * Example 7 - Shows how to translate ontology to a different namespace (removed in 1.0) |
| | 20 | |
| | 21 | == Additional use cases == |
| | 22 | * [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 |
| | 23 | * [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 |
| | 24 | * [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 |
| | 25 | * [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 |
| | 26 | * [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 |
| | 27 | * [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 |
| | 28 | * [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 |
| | 29 | * [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 |
| | 30 | * [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 |
| | 31 | |
| | 32 | == Reasoning == |
| | 33 | (see [wiki:Reasoning more info]) |
| | 34 | * [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 |
| | 35 | * [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) |
| | 36 | |
| | 37 | 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]. |
