def filter_cdb_by_icd10(cdb: CDB) -> CDB:
"""
Filters an existing CDB to only contain concepts that have an associated ICD-10 code.
Can be used for snomed orr UMLS CDBs.
:return: filtered CDB
"""
cuis_to_keep = [cui for cui in cdb.cui2names.keys() if 'icd10' in cdb.cui2info[cui]]
cdb.filter_by_cui(cuis_to_keep)
return cdb
def _create_cat(self):
"""
Loads MedCAT resources and creates CAT instance
"""
if os.getenv("APP_MODEL_VOCAB_PATH") is None:
raise ValueError(
"Vocabulary (env: APP_MODEL_VOCAB_PATH) not specified")
if os.getenv("APP_MODEL_CDB_PATH") is None:
raise Exception(
"Concept database (env: APP_MODEL_CDB_PATH) not specified")
# Vocabulary and Concept Database are mandatory
self.log.debug('Loading VOCAB ...')
vocab = Vocab()
vocab.load_dict(path=os.getenv("APP_MODEL_VOCAB_PATH"))
self.log.debug('Loading CDB ...')
cdb = CDB()
cdb.load_dict(path=os.getenv("APP_MODEL_CDB_PATH"))
# Apply CUI filter if provided
if os.getenv("APP_MODEL_CUI_FILTER_PATH") is not None:
self.log.debug('Applying CDB CUI filter ...')
with open(os.getenv("APP_MODEL_CUI_FILTER_PATH")) as cui_file:
all_lines = (line.rstrip() for line in cui_file)
selected_cuis = [line for line in all_lines
if line] # filter blank lines
cdb.filter_by_cui(selected_cuis)
# Meta-annotation models are optional
meta_models = []
if os.getenv("APP_MODEL_META_PATH_LIST") is not None:
self.log.debug('Loading META annotations ...')
for model_path in os.getenv("APP_MODEL_META_PATH_LIST").split(':'):
m = MetaCAT(save_dir=model_path)
m.load()
meta_models.append(m)
return CAT(cdb=cdb, vocab=vocab, meta_cats=meta_models)
