def add_obo_hierarchies(self):
from indra.databases import obo_client
namespaces = ['go', 'efo', 'hp', 'doid', 'chebi']
edges = []
rel_mappings = {
'xref': 'xref',
'isa': 'isa',
'partof': 'partof',
'is_a': 'isa',
'part_of': 'partof',
# These are for ChEBI: identical to the old behavior but it might
# make sense to add other relations here too
'is_conjugate_acid_of': 'isa',
'has_functional_parent': 'isa',
'has_parent_hydride': 'isa',
'has_role': 'isa'
}
for ns in namespaces:
oc = obo_client.OboClient(prefix=ns)
for db_id, entry in oc.entries.items():
for rel, targets in entry.get('relations', {}).items():
# Skip unknown relation types
mapped_rel = rel_mappings.get(rel)
if not mapped_rel:
continue
for target in targets:
edges.append((self.label(ns.upper(), db_id),
self.label(ns.upper(), target),
{'type': mapped_rel}))
self.add_edges_from(edges)
def add_obo_nodes(self):
from indra.databases import obo_client
namespaces = ['go', 'efo', 'hp', 'doid', 'chebi']
nodes = []
for ns in namespaces:
oc = obo_client.OboClient(prefix=ns)
for db_id, entry in oc.entries.items():
nodes.append((self.label(ns.upper(), db_id),
{'name': entry['name']}))
self.add_nodes_from(nodes)