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You posted your question inside the Oracle Designer Headstart forum. It's is not the correct forum for your question, but I can give you the following answer.
The tool you are looking for is Oracle Designer and is part of the Oracle Developer Suite. In Oracle Designer you make ERD's and DFD's and it has a repository inside the oracle database where your entities and relationships are stored.
There is also the tool called SQL Developer Data Modeler. SQL Developer Data Modeler is a free data modeling and design tool, proving a full spectrum of data and database modeling tools and utilities, including modeling for Entity Relationship Diagrams (ERD), Relational (database design), Data Type and Multi-dimensional modeling, with forward and reverse engineering and DDL code generation. SQL Developer Data Modeler has the option to use subversion as a file based repository.
If you have more questions about SQL Developer Data Modeler(SQL Developer Data Modeler or Oracle Designer (Designer please post them in the corresponding forums.