parsing ontologies

ontology_fun.py

import json
from allensdk.core.structure_tree import StructureTree

file_name = "C:/Users/davidf/Downloads/mouse-brain-ontology.json"
structures = json.load(open(file_name,'r'))

# workaround for a bug in StructureTree.clean_structures that I just found
for s in structures:
    s['id'] = int(s['id'])
    s['structure_sets'] = []
    
# clean up the input to what StructureTree wants
clean_structures = StructureTree.clean_structures(structures)

# Make a StructureTree
st = StructureTree(clean_structures)

visp = st.get_structures_by_acronym(['VISp'])[0]
print visp['name']
print visp['id']

print "children of visp"
visp_children = st.children([visp['id']])[0]
print visp_children

print "parent of visp"
visp_parent = st.parent([visp['id']])[0]
print visp_parent