Persistent data is information that can outlive the program that creates it. The majority of complex programs use persistent data: GUI applications need to store user preferences across program invocations, web applications track user movements and orders over long periods of time, etc.
Transparent persistence is the storage and retrieval of persistent data with little or no work from you, the developer. For example, Java serialization is a form of transparent persistence because it can be used to persist Java objects directly to a file with very little effort. Serialization's capabilities as a transparent persistence mechanism pale in comparison to those provided by JDO, however. The next chapter compares JDO to serialization and other available persistence mechanisms.