New format for Dictionary

[bjonnh]

I would like to discuss a simpler and less redundant format for the dictionary, there are several options, one would also be to put that in RDF or JSON-LD so it can be used as a real ontology.

I was envisioning something more like:

{"version": "1.0",
 "schema": "http://…",
 "data": {"pathways": <PATHWAYS>,
              "superclass": <SUPERCLASSES>,
              "classes": <CLASSES> }
}

Where <PATHWAYS>

[{"id": 0, "name": "Alkaloids"},
 {"id": 1, "name": "Amino acids and Peptides"}]

<SUPERCLASSES>

[ {"id": 1000, "name": "Alkylresorsinols", "parent": 4},
  {"id": 1001, "name": "Amino acid glycosides", "parent": 1}]

<CLASSES>

[ {"id": 10000, "name": "12-oxophytodienoic acid metabolites", "parent": "1043"},
  {"id": 10001, "name": "2-arylbenzofurans", "parent": "1029"} ]

There are several aspects here:

• All the ids will be unique, even for different objects (that's how we do it with ontologies)
• Every object defines its parent directly in its definition, so there is no redundancy (for now the schema puts again all the pathways for every superclass of classes and it is separate from their definitions).