"Cup of water" isn't a great example because it would imply then cup was made from water. This makes more sense when you realize "cup of water" is lazy speech for "cup full of water".
"of" usually implies a state of being while "from" implies a transformation.
"JS of Ocaml" implies that the JS is Ocaml, but that's not true as it is transformed. "JS from Ocaml" would be more accurate.
The of in Cup of water act as a normal genitive. It communicates that the cup relates to water and the only reasonable relation between a cup and an edible liquid is that the cup contains the liquid
