How should the graph look like?

If you draw it on paper, it looks natural.

If you make it out from the matches and jar – it looks natural, too.

And the text is somewhat cumbersome. Trees show beautifully (JSON, s-expressions and others). Lists – even simpler. But what about graphs?

Yes, you can use names and references (most of programming languages, YAML, etc).

Is there any other methods?

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