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Compile and run the Protege 4 OWL editor from Eclipse

This document is in progress. While it is not fully documented yet it does represent the recommended way to set up a protege 4 environment in eclipse. If this documentation is insufficient the fall back is to go to the generic ide instructions.

  1. Download the protege plug-ins with linked source. Currently these can be found [[1]] but soon there will be a standard download page connected to each of our releases.
  2. Create a new eclipse workspace
  3. Click "File -> Import..." This will bring up a dialog box.
  4. Choose "Plug-in Development -> Plug-ins and Fragments" and click "Next". This will bring up a dialog box.
  5. Unselect "The target platform (as specified in the Preferences)"
  6. Click the browse button and browse to the directory where you downloaded the protege plug-ins with linked source
  7. Don't worry about the warning at the top of the dialog box. The "Plug-ins and Fragments to Import" box should say "Select from all plug-ins..." and the "Import As" box should say "Binary projects".
  8. Click next bringing up a new dialog box.
  9. Click "Add All". You should see the following plugins
    • org.protege.common.jar (mandatory)
    • org.protege.editor.core.appllication.jar (mandatory)
    • org.protege.editor.owl.jar (mandatory)
    • org.semanticweb.owl.owlapi.jar (mandatory)
    • com.owldl.pellet (optional)
    • org.coode.dlquery (optional)
    • (optional)
  1. Click "Finish"

This is a milestone. You should now see the Protege bundles as imported Plug-in projects.

Creating a Runnable for Windows or Linux

We now need to create a runnable. As far as I can tell Mac users cannot get the following steps to work. It is that this does work on intel macs but I have not been able to test this. There are claims made on the web saying that this issue is solved. ... Here ... is my current status on this issue. Mac users need to use an alternative method.

Windows and Linux users now do the following to make a runnable.

  1. Click "Run -> Debug Configurations". This will bring up a dialog box.
  2. Select "OSGi Framework" and click the "New" Icon at the top.
  3. Name the "New_Configuration" something useful like "Protege".
  4. In the Bundles box, scroll down to where it says "Target Platform". Unselect all the bundles from the target platform (one click to the left of "Target Platform")
  5. Click on "Add Required Bundles".
  6. Click "Apply" to save your changes.
  7. Click "Debug" and Protege should come up.

Windows and Linux users should now be able to easily use eclipse to develop their plug-ins. To start a new bundle just create a new Eclipse Plug-in project. These projects will automatically get attached to the Protege runnable.

Creating a Runnable for OS X

OS X users have to work a bit harder to get a working runnable. They need to checkout the ide project as a general project from svn at Then they must

  1. Set the working directory to ${workspace_loc:ide}.
  2. Set the classpath to be ide/org.eclipse.osgi.jar
  3. Set the -D vars

At this point, mac users can create Eclipse Plug-in projects to create their own plug-ins. But the

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