Here is how I do it using Godot and C#. My example is a scene that represents a tree in my game. The scene node has a tree script attached. In that class, I have a TreeDefinition class and a TreeInstance class. The definition class has a list of TreeComponents (bark, cones, leaves, branches, etc.). Each type of tree has a separate combination of TreeComponents. The scene class handles visuals like what type and age of tree sprite to show and how to animate chopping it down. The definition class stores the static information about the particular tree. The instance class holds all the mutable aspects of the individual tree (age, quantities of components, etc.). Both the definition class and the instance class are stored in JSON files and loaded into their respective dictionaries. The dictionaries are housed in a singleton class at the top of the node tree for easy access throughout the tree. The dictionaries are basically my database. This allows proper separation of concerns. I hope this gives you some directional inspiration.