Fixing a Display Bug in Protégé

Your dear author is learning how to create an ontology for a sub-set of GeneNetwork data. To make his work easier, he searched for a GPL-compliant tool that can: 1) Generate a graph; and 2) export the ontology to different formats. This adventurous journey led him to stumble upon: Protégé. This desktop application tool hasn’t been packaged yet in GNU Guix upstream—something to do with how notoriously difficult it is to package Java projects—but is however provided in the official Arch Linux repositories.

Installing the tool in Arch Linux was easy:

sudo pacman -S protege

After installation, your beloved author ran into an annoying issue where the program started off with a blank window:

Luckily for your author, this is a well known issue with a straight-forward solution; simply run “protege” with some special flag like so:

_JAVA_AWT_WM_NONREPARENTING=1 protege

Should you face a similar problem, you can stick this flag in one of your start-up dotfiles.

Your author will be reporting on his experience with creating ontologies; hopefully relevant material to you!