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Download Protege 5.5 and View Mondo Files (Windows)

Operating system

These are instructions for PC

Protege version

As of August 2019, Mondo editors are using Protege version 5.5.0

Download and install Protege

These instructions are adopted from here

  1. Go to the download page and click the Download button.
  2. Once the download completes, navigate to the folder where Protégé was downloaded to. This will typically be your “Downloads” folder. For example, “C:/Users/[your-username]/Downloads”.
  3. Right-click on the Protégé file and choose Extract All… from the popup menu to launch the Extract Compressed Folders dialog.
  4. Click the “Browse…” button to select a destination for your Protégé Desktop installation, e.g., the “C:/Program Files” folder:
  5. Protege Desktop will be extracted to your selected destination into a folder called “Protege-5.5.0”.
  6. There are two ways to launch Protégé: (1) Double-click on the Protege.exe, or (2) Double-click on run.bat - which will start Protege also showing the console.
  7. For quicker access to Protege Desktop going forward, right-click on the Protege.exe file and select “Send to” -> “Desktop (create shortcut)”. This will create a shortcut to Protege Desktop’s launcher on your Windows Desktop.

Download and install GitHub desktop

  1. Download GitHub Desktop from this link

Clone the Mondo repository from GitHub

  1. Open the GitHub repository where the ontology you want to clone lives, in this case, Mondo GitHub repository
  2. Click Code


  1. Click 'Open with GitHub Desktop'


  1. You will be given an option as to where to save the repository. I have a folder called 'git' where I save all of my local repos.
  2. This will open GitHub Desktop and the repo should start downloading. This could take some time depending on the size of the repository.

Open the Ontology in Protege

  1. Open Protege
  2. Go to: File -> Open
  3. Navigate to mondo/src/ontology/mondo-edit.obo and open this file in Protege. Note, this is the non-released version of Mondo which is being edited by the Mondo development team. You can see the latest changes in this file.
  4. To view the released version, go to mondo/mondo.obo