Protege4GettingStarted

Getting Started with Protege-OWL

This page contains instructions for getting started with the Protege-OWL editor in Protege 4.0.

Download

If you haven't already done so, you need to download and install Protege 4.0 from the Protege website. If you are a new user, please go to the main download page and register first, which helps us to track the number of Protege users: http://protege.stanford.edu/download/download.html.

If you are an existing user, you can proceed directly to the installer page: http://protege.stanford.edu/download/prerelease-alpha/index.html.

Note: On the main download page, you will also find links to a release notes page for each new build of Protege 4.0, as well as a link to the location of the source code: http://protege.stanford.edu/download/registered.html#p4.

screenshot of protege 4.0 installer page

Install & Run Protege

Once you have navigated to the installer page, click the "Download Installer for <xxx-platform>" button to run the installer:

screenshot of protege 4.0 installer

Run Protege from the location where you installed shortcuts or from the Protege installation directory specified during the installation process. On a Windows machine, you can double-click the Protege executable file (Protege.exe), or use the run batch file (run.bat). If you choose to use the batch file, please make sure the JAVA_PATH variable is set correctly. On the Mac there will be a Protege.app, or you can run using one of the scripts. Note: by default, Protege 4.0 is configured to run in a fairly small memory footprint ~200MB. To get optimum performance, you can change this using our instructions on setting the heap size.

You will now be presented with the Welcome screen from which you can create a new ontology or open an existing ontology from your local machine or from the Web. We can start by opening an existing ontology. Note: once you have opened or saved an ontology, it will be easily available to click on in the "Open Recent" box.

screenshot of protege 4.0 welcome screen

Download the pizza ontology from http://www.co-ode.org/ontologies/pizza (the unclassified version in RDF syntax will work as an example).

Select Open OWL ontology from the Welcome screen and find the pizza.owl file on your filesystem.

You will now be presented with the main Protege workspace, which opens by default to the Active Ontology. This tab shows an overview of the pizza ontology, including metrics on its contents, annotations about the ontology as a whole, and other imported ontologies (if any imports exist). The dropdown on the toolbar displays the currently active ontology - that is the one into which all edits take place. When working on a single ontology this is not a concern. To find something interesting now switch to the Entities Tab

   

 

   

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The entities tab is the workhorse of the ontology editor. From here you can explore all of the classes, properties and individuals in an ontology. As you may have already noticed each tab is made up of several views which can be resized, removed, floated, split and layered - more about views later. The selection model is global, so when a class, property or individual is selected in the trees on the left hand side, the right pane changes to display the selection immediately. In addition most views implement hypertext navigation so that links can be followed easily regardless of which view the user is in. Opening up the hierarchies and selecting a class or property displays the appropriate description on the right. Backward and forward navigation is possible with the left and right arrow buttons in the toolbar, which act just like a web browser.

Another easy way to navigate around the contents of the ontology is to perform a search. The find box in the toolbar performs a global search over any named entity in the ontology. In addition, the hierarchy views have their own find dialogs (first click anywhere in the view to give it focus, then Ctrl-F on windows, Command-F on mac).

Note that several views are stacked on top of each other. For example,the annotations view has an additional view hidden underneath - the Usage view. Show this by clicking on the faint tab underneath the view.

Reasoning with your ontology is one of the most common activities and Protégé 4.0 comes with 2 reasoners built in, FaCT++ and Pellet. To classify your ontology, open the Reasoner menu and select one of the available reasoners. FaCT++ will automatically classify your ontology. Pellet requires that you select classify. Once you have done this the class hierarchy on the entites tab changes to show the inferred class hierarchy. Unsatisfiable classes appear in red under Nothing and everything else appears in the hierarchy under their inferred superclasses. The asserted class hierarchy is still available, stacked under the asserted one.

Investigate the other tabs:

• OWLViz - requires installation of Graphviz before anything will be visible. Shows a graphical representation of the class subsumption hierarchy. A full description of OWLViz is in the OWLViz manual.
• DL Query - requires the ontology has been classified before it will return results. An arbitrary class description can be entered and the reasoner is queried for the sub/super classes, infered members etc depending on what is selected.

Reconfiguring the interface is easy. Adding and removing tabs and views is possible through the tabs and view menus. Try removing the Classes, and Properties views to declutter the screen. Try adding a view to the Entities tab:

1. Select a class to make sure the Selected Entity view is showing class views.
2. Select View->Class Views->Existential Tree - now when you float over the editor a blue outline shows where the new view will be dropped - either on top of, above, below, left or right of each of the current views.
3. When happy with the position, click the left mouse button to drop the view (if you want to cancel this operation just click somewhere on the toolbar instead).
   
   
   
4. The existential tree view is now visible (the tree follows existential restrictions along the specified properties and is useful for partonomic relations).

All changes will be saved when Protégé is shut down properly (or this can also be forced by selecting Save Current Layout in the Tabs menu).

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