Hi,

You don't need to worry much on the underlying of the datastore (big table) 
but rather understand how the datastore works as a non relational way of 
persisting data in your application. If you are using Java you have:

- JPO: http://code.google.com/appengine/docs/java/datastore/jdo/
- JPA: http://code.google.com/appengine/docs/java/datastore/jpa/

There are also other frameworks that you can check out:
- Objectify: http://code.google.com/p/objectify-appengine/
- slim3: http://code.google.com/p/slim3/
- Twig: http://code.google.com/p/twig-persist/

I will recommend to start by reading about the Datastore: 
http://code.google.com/appengine/docs/java/datastore/overview.html getting 
familiar with its concept (keys, properties, entities, ancestors ...) 

Another good resource of information would be Past Google IO talks:
- http://www.youtube.com/watch?v=2jW2iSKDipY

For the scenario you picture on your example, you are right you can not do 
join queries. A workaround would be to de-normalize your data model to have 
the department information within the employee entity, so you could make a 
query over the kind employee.

Hope this helps you getting started on Datastore and App engine. If you have 
more questions don't hesitate to ask!

Happy coding!

Best,
Jose Montes de Oca

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