def add_mesh_parents(bio_ontology: BioOntology):
"""Add missing root level nodes to the MeSH ontology."""
for letter, name in mesh_roots_map.items():
bio_ontology.add_node(bio_ontology.label('MESH', letter), name=name)
edges_to_add = []
for node in bio_ontology.nodes():
# First deal with subtree root nodes
subtree = is_mesh_subroot_node(bio_ontology, node)
if subtree is not None:
edges_to_add.append((
node,
bio_ontology.label('MESH', subtree),
{'type': 'isa'}
))
db_ns, db_id = bio_ontology.get_ns_id(node)
# Then deal with supplementary concepts
if db_ns == 'MESH' and db_id.startswith('C') \
and db_id != 'C': # To skip the previously added subroot node
edges_to_add.append((
node,
bio_ontology.label('MESH', 'S'),
{'type': 'isa'}
))
bio_ontology.add_edges_from(edges_to_add)
def add_ido_parents(bio_ontology: BioOntology):
ido_root = bio_ontology.label('IDO', '0')
bio_ontology.add_node(ido_root, name='infectious disease concept')
edges_to_add = []
for node in bio_ontology.nodes():
if bio_ontology.get_ns(node) == 'IDO' and not \
bio_ontology.get_parents(*bio_ontology.get_ns_id(node)):
edges_to_add.append((node, ido_root, {'type': 'isa'}))
bio_ontology.add_edges_from(edges_to_add)
def add_chebi_parents(bio_ontology: BioOntology):
"""Add missing root level nodes to the ChEBI ontology."""
chebi_root = bio_ontology.label('CHEBI', 'CHEBI:0')
bio_ontology.add_node(chebi_root, name='small molecule')
edges_to_add = []
for node in {'CHEBI:CHEBI:24431', 'CHEBI:CHEBI:36342',
'CHEBI:CHEBI:50906'}:
edges_to_add.append((node, chebi_root, {'type': 'isa'}))
bio_ontology.add_edges_from(edges_to_add)