Graphs are a natural way to express structures, of things being composed of parts which are somehow related to each other connected to each other. What are som

Graphs are a natural way to express structures, of things being composed of parts which are somehow related to each other connected to each other. What are some alternatives to graphs? Well some kind of language, say a programming language. But underlying any program written in any programming language is a graph of the parts of the program and their connections to each other. For instance a variable may be written in one section of the code and read in another, and if it is the same variable then those locations in code are part of the graph showing the data-flow of the program. So it is my intuition too that graphs are the fundamental representation of reality as we see it, the parts of reality and the connections and relations between those parts. Knowledge is knowledge about containers and parts and how those related to each other. We can describe it in natural language or perhaps in algebra but really the picture we are expressing in any language is that of wholes and parts and their connections. This is my intuition about it I don't know if such a general intuition is much good in actual theory formation. Theories are graphs I think.