def query_all_kb(self, kb: KnowledgeBase):
"""
Iterate through KB entities, query synonyms and definition, write to file.
:param kb:
:return:
"""
for ent in tqdm.tqdm(kb.entities, total=len(kb.entities)):
mesh_syn, dbp_syn = self.syn_enricher.get_synonyms_to_entity(
ent.aliases)
wiki_ents, definition = self.wiki_enricher.get_definition_to_entity(
ent.canonical_name)
ent.additional_details['mesh_synonyms'] = mesh_syn
ent.additional_details['dbpedia_synonyms'] = dbp_syn
ent.additional_details['wiki_entities'] = wiki_ents
if len(ent.definition) < 5:
ent.definition = definition
kb.dump(kb, self.out_path)
return
def create_umls_kbs(self, entities):
"""
From entity list, create several KnowledgeBase objects with entities from different KBs
:param entities: dict of entities
:return:
"""
for kb_name in constants.TRAINING_KBS:
sys.stdout.write("\tCreating KB %s\n" % kb_name)
kb = KnowledgeBase()
kb.name = kb_name
entities_to_add = entities[kb_name]
for ent_id, ent_val in entities_to_add.items():
new_ent = KBEntity(ent_val['research_entity_id'],
ent_val['canonical_name'],
ent_val['aliases'],
' '.join(ent_val['definition']))
for ent1_id, ent2_id, rel_type, symmetric in ent_val[
'relations']:
rel_id1 = '{}:{}'.format(ent1_id[0], ent1_id[1])
rel_id2 = '{}:{}'.format(ent2_id[0], ent2_id[1])
new_rel = KBRelation(rel_type, [rel_id1, rel_id2],
symmetric)
kb.add_relation(new_rel)
rel_ind = len(kb.relations) - 1
new_ent.relation_ids.append(rel_ind)
kb.add_entity(new_ent)
# write plain KB to json
out_fname = 'kb-{}.json'.format(kb_name)
kb.dump(kb, os.path.join(self.OUTPUT_KB_DIR, out_fname))
# add context to kb and write to file
self.add_context_to_kb(kb)
return