There isn't a feature like this in d3 AFAIK, but you could implement it.

When users indicate that something is a synonym or whatnot, you'd make the change at the model level (i.e in the underlying json/csv data), and then you'd rebind the modified data to re-render the visualization.

For the data persistence for subsequent users; you'd POST the modified bits to your server and store it in your DB.

These are patterns to follow regardless of whether you're using d3 or anything else.

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