I just wanted to post this here in case someone goes looking for an answer in the future
I’ve come across some people asking how to run protégé in nix/nixos
I am able to run it successfully with nix-shel -p jdk8
Then the run.sh file runs no problem. As of this writing, Protege 5.5.0 requires JDK 8 (and not a higher version, nor lower)