`imports.from_file` fails on Allen Mouse Brain Structural Ontology (StructureGraph)

[THinnerichs]

Hey there, thank you very much for already fixing the isolated roots and leaves issue for ontologies given as owl files, which took me some time on my own.

However, I have another issue with your JSON parser. Please run imports.from_file on the Allen Mouse Brain Structural Ontology, throwing an error in the newest nxontology version. Parsed it myself already, but couldn't find a fix to your one.

Best

[dhimmel]

Here's the head of the file at http://api.brain-map.org/api/v2/structure_graph_download/1.json:

{
  "success": true,
  "id": 0,
  "start_row": 0,
  "num_rows": 1,
  "total_rows": 1,
  "msg": [
    {
     "id": 997,
     "atlas_id": -1,
     "ontology_id": 1,
     "acronym": "root",
     "name": "root",
     "color_hex_triplet": "FFFFFF",
     "graph_order": 0,
     "st_level": 0,
     "hemisphere_id": 3,
     "parent_structure_id": null,
     "children": [
      {
       "id": 8,
       "atlas_id": 0,
       "ontology_id": 1,
       "acronym": "grey",
       "name": "Basic cell groups and regions",
       "color_hex_triplet": "BFDAE3",
       "graph_order": 1,
       "st_level": 1,
       "hemisphere_id": 3,
       "parent_structure_id": 997,
       "children": [
        {
         "id": 567,
         "atlas_id": 70,
         "ontology_id": 1,
         "acronym": "CH",
         "name": "Cerebrum",
         "color_hex_triplet": "B0F0FF",
         "graph_order": 2,
         "st_level": 2,
         "hemisphere_id": 3,
         "parent_structure_id": 8,
         "children": [
          {

This doesn't look like OBO Graphs JSON which is the only JSON format from_file supports.

From Allen's page downloading an Ontology's StructureGraph, it appears that they are calling this format a "StructureGraph". I don't think this is a standard graph or ontology encoding format.

Parsed it myself already

Sounds like you've already written a parser for this format. You can always use your parser to import to nxontology or networkx:

from nxontology import NXOntology
nxo = NXOntology
# add nodes
for node in nodes:
    nxo.add_node(node)
# add edges
for parent, child in edges:
    nxo.add_edge(parent, child)

If you want a more permissive constructor with greater chance for bugs, you can do:

import networkx as nx
graph = nx.DiGraph()
# add nodes
for node in nodes:
    graph.add_node(node)
# add edges
for parent, child in edges:
    graph.add_edge(parent, child)
nxo = NXOntology(graph)