Protege 3.5 has an issue with MySQL v5.6 and higher where the length (in bytes) of the short_value column is insufficient. The resolution is to set this to 255 (the limit for UTF-8 text columns when they are used in indexes). The beauty of Protege is that we can do this without having to make any code changes - just by setting two properties in the file.

  • Go to File -> Preferences and go to the ‘’
  • Create a new property called: and set the value to 255 
  • Create another new property called: and set that value to VARCHAR(255)

Now, when you perform the Convert to Protege Database, the short_value column will be adjusted and the project will save in to a MySQL 5.6+ table