I'm building a 3D database that lets you explore graph and relational data that you've created. For research or creating your own mind palaces - you can freely join & filter collections of information. But it's more like a 3D excel of sorts.
I'm curious what you're using to build this. I've been playing around with a similar idea, and have been prototyping in Godot. Visually representing the connections/structures between items has been a sticking point, but I've settled on two main abstractions: stacks and surfaces, mapping to 1D and 2D arrangement. I've been hesitant to explore 3D, as it unlocks many novelties in the design of a micro-world; but I do think that a 3D space brings a lot of our instincts from the physical world into digital ones. Would be curious to hear how you're approaching the problem, if you feel like sharing.
For what i'm after, 3D is the only way to go. I'm building it in unity so you can store markdown, webpages, video and images within 3D space and relate them to each other. (so not really a tool for visualizing a production DB or anything)