iBooks for Mac automatically moves your book library from iTunes
over to the iBooks for Mac app. When you browse your Book library in
iTunes 11.1 or later, iTunes notifies you that your books have been
moved to iBooks for Mac. After clicking OK, you no longer see Books as a
category in the media list in iTunes. Future book purchases made from
the iBooks Store through iTunes or iBooks are downloaded to your iBooks
library instead of iTunes.