Rule-Based Mediation for Model Annotation: Running the Java Code

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For expert users only. Currently in flux.

Included is Java code which runs the Pellet reasoner over the asserted ontology and saves the inferred ontology to a new file. In order to make use of this code, you need the following tools:

  1. Maven 2.0 or higher. Maven is used to build the Java project.
  2. OWLAPI 2.2.0. The OWLAPI can be built as a Maven project, though its jars are not available in any public Maven repository. Follow the instructions in the link to install and place in your local Maven repository.
  3. Pellet 2.0.0-rc7. Once you've downloaded the jar, unzip and then run the install file commands visible in this project's pom.xml to get the new jar into the Maven repository. If you have a different version of Pellet, simply change the ${pellet.version} property in this project's pom.xml.
  4. MFO Jar. You also need to compile and include in your Maven repository the latest version of the MFO toolset.

Once you have the supporting software, you need to run the class uk.ac.cisban.rbm.ReasonOverIntegratedSchema. This class assumes that the location of the ontologies to import is the same as is provided in the subversion version of is-container.repository. Please update ReasonOverIntegratedSchema as needed to reflect any changes you might make.

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