For a software project I am working on, I have developed an ontology which 
I have represented in JSON data format rather than the standard OWL/RDF 
formats. The reason for this is because I wanted to use the amazing DS3.js 
library to visually display the ontology. This is all working fine.

But now the User has made some additional requests which I am struggling 
with. These are:

   1. To use the same JSON file to describe where in the User's database 
   the data that represents the ontological entity resides. For example, if 
   there was an entity in my ontology called Wine, there would be a 
   corresponding table in the database holding a record for each type of wine.
   2. To use the same JSON file to generate POJOs for each ontology entity. 
   Since the ontology has a tree like structure, this is corresponds to a Java 
   class heirarchy.

My initial thoughts are to use a graph database (Neo4j) to build the 
connection/relationships between the ontology entity and where the data in 
the database resides. But then I would have duplicated my effort because 
the ontology data would then be both in the JSON file and in Neo4j.

To summarise my questions:

   1. If I use Neo4j to represent my ontology, can I generate the necessary 
   JSON so that the DS3.js library can use it to render the ontology visually?
   2. If the ontology data is in Neo4j, how can I generate the 
   corresponding POJOs and with the necessary Java class heirarchy? But some 
   of the data in Neo4j for each entity should not be used to generate the 
   POJO, namely the attributes which indicate which table in the database this 
   entity is associated with.
   3. Is there a better way to do this? Am I using the right technologies 
   here?

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