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Migrating from a Domino application to an application written in Java that uses an Oracle back-end is a huge undertaking. I've done application designs like this, and the process was always bigger than I anticipated. One of my clients recently migrated from Sybase to Oracle, leaving the Domino application as is. The process took several months.
Here's a brief list of steps for you to take. These should give you an application architecture and migration plan:
Application Review: An overview of the applications goals, requirements, users, support capabilities, etc.
Business Logic Analysis: Document all processes and workflows (i.e. existing forms, views, agents, etc.) to create an application map.
Data Modeling: Produce a database schema from the current Document-based structure of the NSF.
Architectural Modeling: Determine if the application will support J2SE, J2ME and or J2EE.
Infrastructure Analysis: Determine what application server you will be using, as this may determine/provide other components you need (such as the EJB Container for a J2EE application).
I advise you to get experienced help with your plan. If you don't have access to an in-house expert, hire a good consultant -- or you'll pay for it later. Good luck!
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