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)
def add_efo_parents(bio_ontology):
edges_to_add = []
efo_root = 'EFO:0000001'
for node in bio_ontology.nodes():
if bio_ontology.get_ns(node) == 'EFO' and \
not bio_ontology.get_parents(*bio_ontology.get_ns_id(node)):
edges_to_add.append((node, efo_root, {'type': 'isa'}))
print('Adding %d EFO isa edges.' % len(edges_to_add))
bio_ontology.add_edges_from(edges_to_add)
def add_drugbank_parents(bio_ontology):
edges_to_add = []
drugbank_root = 'DRUGBANK:DB00000'
bio_ontology.add_node(drugbank_root, name='Drugs')
for node in bio_ontology.nodes():
if bio_ontology.get_ns(node) == 'DRUGBANK' and \
not bio_ontology[node]:
edges_to_add.append((node, drugbank_root, {'type': 'isa'}))
print('Adding %d DRUGBANK isa edges.' % len(edges_to_add))
bio_ontology.add_edges_from(edges_to_add)
def add_protein_parents(bio_ontology):
"""Add parent categories for proteins in the ontology."""
# Add root nodes for human and non-human proteins
human_root = 'INDRA:HUMAN_PROTEIN'
non_human_root = 'INDRA:NON_HUMAN_PROTEIN'
bio_ontology.add_node(human_root, name='Human protein')
bio_ontology.add_node(non_human_root, name='Non-human protein')
# We add each category as a node and link them to the human protein
# root
edges_to_add = []
for category_name, category_label in category_map.items():
bio_ontology.add_node(category_label, name=category_name)
edges_to_add.append((category_label, human_root, {'type': 'isa'}))
# Now we go over the whole ontology, and add extra edges
for node in bio_ontology.nodes():
# If this is a protein family and doesn't have any further FamPlex
# parents then we find its specific protein children, look at all
# their categories, and add links from this node to the nodes of
# these categories.
if is_protein_family(bio_ontology, node):
# Skip if this has further FPLX parents
if has_fplx_parents(bio_ontology, node):
continue
else:
# Get child categories
categoriesx = get_categories(node)
# If there are no categories, link directly to human protein
# root
if not categoriesx:
edges_to_add.append((node, human_root, {'type': 'isa'}))
else:
# If there are categories, we link this family to each
# of those
for category in categoriesx:
edges_to_add.append((node, category_map[category], {
'type': 'isa'
}))
# If this is a specific human protein and doesn't have any FamPlex
# parents then we link it to either a category node or the root node
elif is_human_protein(bio_ontology, node):
if has_fplx_parents(bio_ontology, node):
continue
category_node = get_category(node)
# If there is a caqtegory, we link to that, otherwise to
# the human protein root
if not category_node:
edges_to_add.append((node, human_root, {'type': 'isa'}))
else:
edges_to_add.append((node, category_node, {'type': 'isa'}))
elif is_non_human_protein(bio_ontology, node):
edges_to_add.append((node, non_human_root, {'type': 'isa'}))
bio_ontology.add_edges_from(edges_to_add)
def add_protein_parents(bio_ontology):
human_root = 'INDRA:HUMAN_PROTEIN'
non_human_root = 'INDRA:NON_HUMAN_PROTEIN'
bio_ontology.add_node(human_root, name='Human protein')
bio_ontology.add_node(non_human_root, name='Non-human protein')
edges_to_add = []
for node in bio_ontology.nodes():
if is_human_protein(bio_ontology, node):
edges_to_add.append((node, human_root, {'type': 'isa'}))
elif is_non_human_protein(bio_ontology, node):
edges_to_add.append((node, non_human_root, {'type': 'isa'}))
bio_ontology.add_edges_from(edges_to_add)