> JavaScript Object Notation which looks exactly the same as JavaScript.
Whether it looks the same is irrelevant. It doesn't even have the same syntax rules. For example, this is valid JavaScript:
{
one: "two",
three: undefined
}
... but would be completely invalid in JSON, in more than one way. No, they are not the same.
> don't see how it's the same as converting for example PHP to MySQL where I'm bound by a schema which looks nothing like my data structure in PHP
And in 99% of cases, this is a feature, because you can't represent most data as a flat list of nested objects. See also this article: http://www.sarahmei.com/blog/2013/11/11/why-you-should-never...
Aside from that, if you want a native nested representation of data in your database, so including relations, you use an ORM. For example, in PHP with MySQL, you might use Eloquent.
How data is represented in your application and how it's represented in the database, are two entirely different things. There's no advantage to be gained from trying to make them the same thing - that's the concern of the database abstraction that you choose to use.
