I'd like to have something that I can record all the schemas in and then cross reference them, so I can ask things like, "which collections contain links to bigmongo.user.id?" or "if I delete one record from table X, what are all the other records I'm going to have to delete?"
Have you heard of such a beast, or am I going to somehow have to roll my own with neo4j, datatomic, or prolog?
If you are looking for schema change management tool, then you can check out Bytebase (bytebase.com). But it can't answer questions like "which collections contain links to bigmongo.user.id?"