Best pattern or strategy to store Diagrams (and Models)?

We are developing a simple Modeling Tools (to use it in other refactoring tools) to manage diagrams like CDG (Call Dependency Graph between classes) and etc.

Our diagrams are similar to UML diagrams and they have some details like Use Case or Class Diagram's details.

In this project we should store diagrams and open them later for some changes by users. (Similar to other modeling tools)

Basic Implementation of this tools in Java are here:
http://ift.tt/2jvLpw3

The Question is: What is the best way to store a diagram? Which patterns exist to do this (and our team should learn them)?

Two factors are important:
1- performance of reading and writing diagrams.
2- diagram size on the hard/server.