87 
 
You might be tempted to resolve this thread (note the Resolve link at the top of the initial comment) 
however, we aren’t really done. Remember that we need to not just create the class but also define the 
axiom that a ChicagoPizza must have a DeepPanBase. Since we can’t add axioms in Web Protégé we 
need to export our ontology back to Protégé. Typically, we would collect many more comments and 
changes before exporting but we want to demonstrate how round-trip editing works between Protégé and 
Web Protégé. We could of course just export the ontology from Web Protégé to Protégé and then create 
another new Project, but it would be cumbersome to have to constantly create new projects every time 
you want to make a change in Protégé and if we did this, we would lose our audit trail of comments and 
changes. Luckily, there is a better way to do it.  
To start we need to export the ontology to a file. Note that one of the tabs at the top is History. Select that 
tab. This tab shows a list of each version of the ontology. There should be 2 versions labelled R1 and R2 
(in the right corner of each version). The most recent version is always at the top since that is typically 
what you want although it is also possible to roll back changes to previous versions. We want to export 
the latest version R2. Click on the R2 icon. This should give you a drop-down menu with two options: 
Revert changes in revision 2 and Download revision 2. Select Download revision 2. This will prompt you 
with the standard file browser for your OS to save a zip file with the new ontology. The ontology is saved 
with a zip file because ontologies can be large and since Web Protégé is working over a network we may 
want to limit the network traffic for large ontologies. Select the appropriate place to save the Zip archive 
file on the machine where you have Protégé. Do the standard things you would do to unzip the file and 
load it into Protégé. Note that when you unzip the file it will create a directory as well, so the file won’t 
be directly under whatever directory you save it to. Instead, there will be a directory titled something like 
pizza-with-data-ontologies-owl-REVISION-2 that the OWL file will be in.  
Load the downloaded file into Protégé. Go to the Class hierarchy tab and navigate to the new 
ChicagoPizza class under NamedPizza. Add the axiom (refer back to chapter 4 if you need to remember 
how to add axioms to classes) hasBase some DeepPanBase. Save the file. Now go back to Web Protégé 
and your version of the Pizza ontology there. Note that in the upper right corner of the window there are 
links (drop down menus) such as Display and Project. Select Project and from the drop down menu select 
Apply External Edits. This will give you a small dialog titled Upload ontologies with a little button to 
Choose File.  Click on Choose File. That will give you the standard OS dialog for selecting a file. 
Navigate to the file you saved from Protégé and select that then choose OK. That should result in a new 
pop-up window titled Merge ontologies where you will see the changes (in this case only the addition of 
the ChicagoPizza axiom) and a text box where you can describe the changes. Add an appropriate 
Commit message or just take the default and select OK. You should get a message that says the changes 
were successfully applied.  
If you navigate back to ChicagoPizza you should see that it now has that axiom. You can also navigate 
back to NamedPizza. In the right most column, you should see the comments about needing to add 
ChicagoPizza as a subclass. Now that this has been done you can click on the Resolve link in the upper 
right corner of the comment thread and the comments will be removed from NamedPizza.