Allowing 3rd party apps to access iBook notes and highlights would be useful, but will probably never happen. It's one of the weak points of the app model that

Allowing 3rd party apps to access iBook notes and highlights would be useful, but will probably never happen. It's one of the weak points of the app model that there's not any good way to work with other programs' data. On the desktop, you could probably write a script to read annotations from a PDF and dump them into something like SuperMemo, but on tablets you need everyone to agree on a format to export so you can email them to yourself. Maybe Android is better about this.