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If you aren't into documentation, a good way to learn how the back end interface works is to look at the backend.h file. Then, look at the small dummy-server in ztest/ztest.c. The backend.h file also makes a good reference, once you've chewed your way through the prose of this file.
If you have a database system that you would like to make available by means of Z39.50, YAZ basically offers your two options. You can use the APIs provided by the Z39.50 ASN.1, ODR, and COMSTACK modules to create and decode PDUs, and exchange them with a client. Using this low-level interface gives you access to all fields and options of the protocol, and you can construct your server as close to your existing database as you like. It is also a fairly involved process, requiring you to set up an event-handling mechanism, protocol state machine, etc. To simplify server implementation, we have implemented a compact and simple, but reasonably full-functioned server-frontend that will handle most of the protocol mechanics, while leaving you to concentrate on your database interface.