I use Graphviz (https://graphviz.org/) for more things than I could possibly recall. It is one of my core tools for data visualization for a wide range of data, and it's quite easy to use and generate graphs for.
If graphs get so large that the visualizations are no longer possible to grok, or if querying is needed, I may opt for a graph database instead.
The graph description language DOT (https://en.wikipedia.org/wiki/DOT_(graph_description_language)) is simple enough to be useful for mapping out thoughts too.
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