Overview

VIVO provides the capability to add ontologies and use them to describe your data and for query.  You can add your own, or pre-existing ontologies.  In each case, the ontology to be added will appear in the VIVO Ontology List along with ontologies provided with VIVO.

Using the Web Interface

Create an Ontology

To create an ontology from the web interface, follow the steps in Create, Assign, and Use an Institutional Internal Class.  These instructions show how to create an ontology using the web interface.  Once your ontology is created, you can add an Institutional Class as described, additional classes, data properties and Object properties.  You may create as many additional ontologies as you need.

Load an Existing Ontology

You can add an ontology from a file into VIVO using the Add/Remove RDF Data feature shown on the Site Admin page.  

Loading from Filegraphs

There is another mechanism for incorporating ontologies into VIVO.  This involves "filegraphs," and is how the VIVO ontology is included with the software.  Filegraphs are RDF documents stored in the VIVO home directory.  Each filegraph corresponds to a single named graph in the triple store.  Every time Tomcat starts, VIVO checks each of these graphs to ensure that its contents exactly match the triples found in the corresponding file.  If the file has changed, VIVO makes the necessary modifications to the corresponding named graph in the triple store.  If a filegraph is removed from its directory, its graph in the triple store will be deleted the next time Tomcat starts.

Example

vivo.home/
    rdf/
        tbox/
            filegraph/
                vivo.owl
                ontologies.owl
                ...
                myOntology.owl
                ...

Adding myOntology.owl to the directory as shown above will automatically create the corresponding named graph in the triple store after Tomcat is restarted:

After restart, go to Site Admin → Ingest Data → Manage Jena Models.  Review the named graphs.  You should see:

Modifying or removing the myOntology.owl file in the filegraph directory and restarting Tomcat will automatically remove the named graph.

Namespace Prefixes

Additional ontologies, whether directly imported via 'Add/Remove RDF data' or implemented as filegraphs, are listed in the ontology list ('Site Admin > Ontology list'). While the ontologies name and namespace are automatically added to the list, the prefix is not. Instead, the note '(not yet specified)' appears. This behavior occurs even if the prefix is correctly specified in the RDF file.

For ontologies that are added to an existing VIVO installation, the prefix needs to be entered manually into the ontology list. If the additional ontology is to be provided with the software before installation, however, the prefix to be added automatically during the build process can be specified beforehand.

VIVO keeps an internal record of prefixes that is read from the /rdf/tbox/firsttime/ directory. The prefixes of the ontologies that are loaded with VIVO are specified in the 'initialTBoxAnnotations.n3' file. You can add an additional prefix by adding the following lines either to this file or to a separate file:

@prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
@prefix vitro:   <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> .
@prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .

<http://*URI/of/the/added/ontology*>
	rdfs:label "*Name of added ontology*" @en-US;
	vitro:ontologyPrefixAnnot "*OntologyPrefix*"^^xsd:string

Of course, the strings enclosed by asterisks need to be adapted according to your custom ontology. After VIVO is built, you should find the new ontology in the ontology list, with its specified prefix.