What do I need to do something like this?

1. User builds a diagram and tags certain boxes and circles with text.
2. User imports diagram into my program.
3. My program processes the tagged boxes and circles and fills them with different colors.
4. My program exports color-filled diagram.

So the questions are...

• What graphics format supports tag-able boxes and circles?
• What existing application should I recommend users to use to produce diagrams in the above format?
• Would this graphics format be very easily readable in code to do things like reading tags and coloring in the associated boxes and circles?

Free / open source libraries and apps are desired as this would be for academic use. Thank you!