The problem with JSON and XML based file formats is the tendency to require further parsing to decode values from strings. A universal interchange file format would have the ability to express all common data types through the composition of atomic values and containers.
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It’s the lack of this notion of local and remote references in data that leaves Java and C# requiring ad hoc database glue layers in languages that were otherwise sufficiently high-level that they could have solved the problem in a wonderfully general way.
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Please look at http://OpenGEX.org . Even if it’s not a perfect fit at the moment, it comes much closer to what you’ve described than anything else, by far. And it’s been battled tested for five years now.
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See: Open Data Description Language http://openddl.org/ , and Open Game Engine Exchange https://opengex.org/ it covers everything you listed here.
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Scheme S-expressions have had support for (internal) pointers/references — necessary, as you note, for cyclic data — for a long time. I was disappointed that neither XML nor JSON borrowed this.
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YAML doesn't seem too bad to me. As far as I remember, it supports typing. Although, YAML can get hairy.
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As soon as there are remote references, you need a unique source of truth on how to get those remotes (even if it could be implicit like the filesystem). this is enlarging the scope of the problem considerably.
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