Convert JSON-LD to D3 force graph? Pin

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I accidentally posted this in the discussions section, moving it to Q/A.

Hi guys,

I'm doing an internship where I'm tasked with working with RDF/OWL ontologies. I've converted an OWL document to JSON-LD, which then I've used to make a tree diagram which wasn't too difficult since there are resources on the net which helped quite a bit.

What I want to do now is convert the JSON-LD data to a format with I can use with the force graph layout in D3. It looks something like this:

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{
  "nodes": [
    {"x": 469, "y": 410},
    {"x": 493, "y": 364},
    {"x": 442, "y": 365},
    {"x": 467, "y": 314},
    {"x": 477, "y": 248},
    {"x": 425, "y": 207},
    {"x": 402, "y": 155},
    {"x": 369, "y": 196},
    {"x": 350, "y": 148},
    {"x": 539, "y": 222},
    {"x": 594, "y": 235},
    {"x": 582, "y": 185},
    {"x": 633, "y": 200}
  ],
  "links": [
    {"source":  0, "target":  1},
    {"source":  1, "target":  2},
    {"source":  2, "target":  0},
    {"source":  1, "target":  3},
    {"source":  3, "target":  2},
    {"source":  3, "target":  4},
    {"source":  4, "target":  5},
    {"source":  5, "target":  6},
    {"source":  5, "target":  7},
    {"source":  6, "target":  7},
    {"source":  6, "target":  8},
    {"source":  7, "target":  8},
    {"source":  9, "target":  4},
    {"source":  9, "target": 11},
    {"source":  9, "target": 10},
    {"source": 10, "target": 11},
    {"source": 11, "target": 12},
    {"source": 12, "target": 10}
  ]
}

My owl ontology is available on pastebin here (in json-ld format): http://pastebin.com/g7ggDyFX[^]. If you take a peak at the context you can see that I'm modelling the ontology by the "isSubClass" property.

I know that to read json files in D3 I can use d3.json. I'm unsure how exactly to convert to the format above though.

I found this github repository https://github.com/uf6/ottograf[^] that says it should be able to convert to the format, but I'm having a lot of trouble running it, and I also want to keep it in javascript. Any tips/solutions? Thanks!