Advanced topic
Please refer to Setup using Universal Studio (KMC) for the recommended setup method.
If setting up Annoto plugin via Kaltura universal studio is not possible, or simply if more customisation is required. It is possible to compile a custom Annoto plugin for the Kaltura player and add it to the player via Javascript.
Please notice, according to Kaltura documentation:
"Flashvar based resource includes will only work on relative paths. You should save absolute external resource URLs to your configuration file for them to work in your production players."
Annoto plugin is an open source and can be compiled into a single javascript file: https://github.com/Annoto/kaltura-plugin