This week's book giveaway is in the OCAJP 8 forum. We're giving away four copies of OCA Java SE 8 Programmer I Study Guide and have Edward Finegan & Robert Liguori on-line! See this thread for details.
JDO has two forms of identity: datastore and application. Application identity is similar to primary keys in a relational database and all the JDO relational implementations support this. With an existing relational schema, you are not likely to have inheritance represented in your tables, so you would typically not have inheritance in your classes. Your foreign keys in the relational schema are mapped to references in your object model. A collection in a class A implies that there are multiple objects associated with it from a class B. At the relational level, this is normally represented by the B table having a foreign key referencing a row in table A (assume a 1-1 between class A/table A, class B/table B). So you can indicate that the foreign key in A serves as the inverse for establishing the collection elements in the collection in B. It is very late and I am tired, so forgive me if I am not making sense. The short answer is that you usually can map existing relational schemas to an object model. Conversely, if you have an existing object model, it is fairly straightforward to map this to a relational schema. You also have the choice of using either datastore or application identity. With datastore identity, the JDO implementation takes care of generating unique identifiers for you. Also when letting JDO generate the relational schema, it can generate the proper table structures to represent inheritance relationships.