README.md

Owlery

Owlery is a set of REST web services, built on the akka-http toolkit, which allow querying of an OWL reasoner containing a configured set of ontologies, via HTTP.

It also provides a web service front-end for Owlet, which can be used as a remote SERVICE in a SPARQL federated query.

Examples

• Phenoscape Owlery api
  • swagger.yaml

Running Owlery

• A docker image is available on DockerHub.
• You can run directly as a Java application: download a .tgz for the latest release.

Configuration

• Configuration file template: https://github.com/phenoscape/owlery/blob/master/src/main/resources/application.conf.example
• Your own configuration file can be specified with a JVM argument, e.g.: -Dconfig.file=/etc/default/owlery.conf

Specifying ontology file(s) to load

The location property for each knowledgebase specifies which ontologies to load into Owlery. This property can be a path or an IRI. If the path is a folder, all files in the folder will be imported into one ontology. If the path is a file, that file will be directly loaded as an ontology. If the value is an IRI, the ontology will be retrieved from that IRI.

Locating ontologies via IRI

By default, an ontology specified by IRI will be downloaded from the web using that IRI. This applies to a location configuration value as well as to any ontologies imported via owl:imports within any loaded ontology. You can use the catalog property for a kb to map ontology IRIs to other URLs or filesystem paths by providing a catalog XML file, as is done in Protégé. For example, application.conf could be:

owlery {
  port = 8080
  host = localhost
  kbs = [
          {
            name = myproject
            location = "http://example.org/my-importer-ont.owl"
            reasoner = hermit
            catalog = "/data/project/catalog.xml"
          }
        ]
}

Say the ontology http://example.org/my-importer-ont.owl contains an owl:imports statement pointing to http://example.org/my-terminology.owl. /data/project.catalog.xml might look like this:

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
    <uri name="http://example.org/my-importer-ont.owl" uri="/data/ontologies/my-importer-ont.owl"/>
    <uri name="http://example.org/my-terminology.owl" uri="/data/ontologies/my-terminology.owl"/>
</catalog>

Experimenting with the API

• The API description can be found on your server. If your server runs locally on port 8080, you can get the API description at http://localhost:8080/docs/swagger.yaml.
• An interactive version of the API can be found here: http://localhost:8080/docs/