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I work with MySQL, and I am using MySQL Workbench, to have a global visualization of my database. The problem is that my database is turning very complex, with lots of tables and relationships, so it is starting to get very messy, I don't know how to organize it in the 2D graphical representation of the model. I was thinking of a 3D system, but maybe I am jumping too far, and there is a simpler way to view/organize my database in a graphical model.

Which software can I use to easily navigate, visualize and design my super complex database with all the tables and relationships?

Should I just do everything through command line?

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I think you should try different approach to your problem - don't try to create huge diagram, human capacity to digest large number of elements is limited. Create more smaller diagrams, each for a specific topic. This is how ERP and CRM providers approach - take out Oracle's eBS Inventory appliaction documentation for instance: https://docs.oracle.com/cd/A88418_01/acrobat/invtrm.pdf

Try documenting your databse with Dataedo - it is a data dictionary creator (enables you to describe each data element) for MySQL, Oracle and SQL Server. It has ability to split large databases into smaller, comprehensible parts called modules. For each module you can create a distinct ER Diagram. You can access it with UI or export it to interactive HTML or PDF.

I'm the product manager of Dataedo.

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Yes stick with the command line (if you have a unix like system). Graphical representations look nice but are not actually more helpful in this case (The 1970s command line is more productive for maybe half of a developers tasks and will likely continue to be)

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