else:
name = current_class.label
cui = None
kg.add_symp_term(current_id, name, cui)
# add relations
for current_class in ontology_classes:
current_id = current_class.name.replace('_', ':')
superclasses = [
x for x in current_class.is_a
if not (isinstance(x, owlready2.entity.Restriction)
or isinstance(x, owlready2.class_construct.And))
]
for superclass in superclasses:
target_id = superclass.name.replace('_', ':')
kg.add_isa_relation(current_id, 'SympTerm', 'symp_id', target_id,
'SympTerm', 'symp_id', 'symp')
# kg = KnowledgeGraph()
# uq = UmlsQuery()
# with driver.session() as session:
# while to_process:
# print(len(to_process))
# current_class = to_process.pop()
# superclasses = [x for x in current_class.is_a
# if not (isinstance(x, owlready2.entity.Restriction) or
# isinstance(x, owlready2.class_construct.And))]
# for superclass in superclasses:
# target_symp_id = superclass.name.replace('_', ':')
# if target_symp_id in id_map:
# cui = id_map[target_symp_id]
# umls_result = uq.cui2bestname(cui)
cui = 'UMLS:' + umls_result[0]['cui']
else:
name = current_class.label
cui = None
kg.add_hpo_term(current_id, name, cui)
# add relations
for current_class in ontology_classes:
current_id = current_class.name.replace('_', ':')
superclasses = [
x for x in current_class.is_a
if not isinstance(x, owlready2.entity.Restriction)
]
for superclass in superclasses:
target_id = superclass.name.replace('_', ':')
kg.add_isa_relation(current_id, 'HpoTerm', 'hpo_id', target_id,
'HpoTerm', 'hpo_id', 'hpo')
# ## get all targets
# with driver.session() as session:
# diseases = get_diseases(session)
# ## loop over targets and get ancestors, then loop until full hierarchy is loaded
# to_process = {obo[record['hpo_id'].replace(':', '_')] for record in diseases}
# processed = set()
# kg = KnowledgeGraph()
# uq = UmlsQuery()
# with driver.session() as session:
# while to_process:
# print(len(to_process))
# current_class = to_process.pop()
cui = id_map[current_id]
umls_result = uq.cui2bestname(cui)
if umls_result:
name = umls_result[0]['name']
else:
name = current_class.label
else:
name = current_class.label
cui = None
kg.add_uberon_term(current_id, name, cui)
# add relations
for current_class in ontology_classes:
current_id = current_class.name.replace('_', ':')
superclasses = [
x for x in current_class.is_a
if not isinstance(x, owlready2.class_construct.And)
]
for superclass in superclasses:
if isinstance(superclass, owlready2.entity.Restriction):
if isinstance(superclass.property(), obo.BFO_0000050):
target = superclass.value().is_a[0]
target_id = target.name.replace('_', ':')
kg.add_part_of_relation(current_id, 'UberonTerm', 'uberon_id',
target_id, 'UberonTerm', 'uberon_id',
'uberon')
else:
target_id = superclass.name.replace('_', ':')
kg.add_isa_relation(current_id, 'UberonTerm', 'uberon_id',
target_id, 'UberonTerm', 'uberon_id', 'uberon')
name = current_class.label
else:
name = current_class.label
cui = None
kg.add_cl_term(current_id, name, cui)
# add relations
for current_class in ontology_classes:
current_id = current_class.name.replace('_', ':')
superclasses = [x for x in current_class.is_a
if not (isinstance(x, owlready2.entity.Restriction) or
isinstance(x, owlready2.class_construct.And))]
for superclass in superclasses:
target_id = superclass.name.replace('_', ':')
kg.add_isa_relation(current_id, 'ClTerm', 'cl_id', target_id, 'ClTerm', 'cl_id', 'cell_ontology')
### deprecated
# uq = UmlsQuery()
# kg = KnowledgeGraph()
# ## get all targets
# terms = kg.get_cl_terms() ## TODO no cl_ids in knowledge graph yet - either map or load full ontology
# ## loop over targets and get ancestors, then loop until full hierarchy is loaded
# to_process = {obo[cl_id.replace(':', '_')] for cl_id in terms}
# processed = set()
# while to_process:
# print(len(to_process))
# add relations
for current_class in ontology_classes:
current_id = current_class.name.replace('_', ':')
superclasses = [x for x in current_class.is_a]
for superclass in superclasses:
if isinstance(superclass, owlready2.entity.Restriction):
if isinstance(superclass.property(), obo.RO_0000087):
target = superclass.value().is_a[0]
target_id = target.name.replace('_', ':')
kg.add_has_role_relation(current_id, 'ChebiTerm', 'chebi_id',
target_id, 'ChebiTerm', 'chebi_id',
'chebi')
else:
target_id = superclass.name.replace('_', ':')
kg.add_isa_relation(current_id, 'ChebiTerm', 'chebi_id', target_id,
'ChebiTerm', 'chebi_id', 'chebi')
# kg = KnowledgeGraph()
# uq = UmlsQuery()
# ## get all drugs
# drugs = kg.get_drugs()
# ## loop over targets and get ancestors, then loop until full hierarchy is loaded
# to_process = {obo[record['chebi_id'].replace(':', '_')] for record in drugs}
# processed = set()
# while to_process:
# print(len(to_process))
# current_class = to_process.pop()
# restrictions = [x for x in current_class.is_a if isinstance(x, owlready2.entity.Restriction)]
cui = 'UMLS:' + umls_result[0]['cui']
else:
name = current_class.label
cui = None
kg.add_go_term(current_id, name, cui)
# add relations
for current_class in ontology_classes:
current_id = current_class.name.replace('_', ':')
superclasses = [
x for x in current_class.is_a
if not isinstance(x, owlready2.entity.Restriction)
]
for superclass in superclasses:
target_id = superclass.name.replace('_', ':')
kg.add_isa_relation(current_id, 'GoTerm', 'go_id', target_id, 'GoTerm',
'go_id', 'go')
# ## loop over targets and get ancestors, then loop until full hierarchy is loaded
# to_process = {obo[record['go_id'].replace(':', '_')] for record in pathways}
# processed = set()
# kg = KnowledgeGraph()
# uq = UmlsQuery()
# while to_process:
# current_class = to_process.pop()
# superclasses = [x for x in current_class.is_a if not isinstance(x, owlready2.entity.Restriction)]
# for superclass in superclasses:
# target_go_id = superclass.name.replace('_', ':')
# umls_results = uq.go2cui(target_go_id)
# if umls_results:
# kg.add_go_term(current_class.name.replace('_', ':'),