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Tagging onto this issue, I ran into the same issue recently. Specifically, when you try to add "New Term" as a node to a query that already has the same category included in one of the nodes, the query edge disappears. I'm pretty sure this is a new issue. There are workarounds, but they are not obvious.
Is it possible to do this query:
(multiple sclerosis)-(chemical)-(gene)-(chemical) and have the two chemicals be different?
When I put chemical entity in that last box it always wants to make it n0
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