Looking for visual imaging/visualization tools to depict 3D graph networks for concept and object mapping

Sorry for cross posting.
I am looking for visual imaging/visualization tools for 3D mapping of concepts and objects.
The 3D vertices/nodes can correspond to either a simple concept or object described as an n-tuple of which the elements are not necessarily specified but can be classified by category theory.
The edges correspond to either state transitions e.g. in (high energy particle physics, topological deformations, transformations, functors, (bio)chemical reaction steps, parsing tree steps, mathematical or logical proof steps, or any part of a sequence in any computer science model used for algorithmic expression.

Milton Ponson
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Aruba, Dutch Caribbean
Project Paradigm: Bringing the ICT tools for sustainable development to all stakeholders worldwide through collaborative research on applied mathematics, advanced modeling, software and standards development