def findDisease(cui, lang):
look_umls = UMLSLookup()
meaning_umls = look_umls.lookup_code_meaning(cui,
lat=lang,
preferred=False)
if meaning_umls:
return str(meaning_umls[0])
else:
#disease = str(all_csv.loc[all_csv['Disease'] == cui]["Disease_UMLS"].unique()[0].encode('utf8'))
print("Using fallback CSV for: " + cui)
return cui
def findSymptom(cui, lang):
look_umls = UMLSLookup()
meaning_umls = look_umls.lookup_code_meaning(cui,
lat=lang,
preferred=False)
if meaning_umls:
return str(meaning_umls[0])
else:
print("Using fallback CSV for: " + cui)
return cui
def findFeatures(cui, lang):
symptom_strings = []
look_umls = UMLSLookup()
for s_cui in getRelatedSymptomsForDisease(cui):
meaning_umls = look_umls.lookup_code_meaning(s_cui,
lat=lang,
preferred=False)
if meaning_umls:
symptom_strings.append(meaning_umls[0])
else:
symptom_strings.append(
all_csv.loc[all_csv['Disease'] == cui]["Symptom"].unique()[0])
return symptom_strings
def getDetails(cui):
look_umls = UMLSLookup()
return look_umls.lookup_code_description(cui)
import csv
from tqdm import tqdm
import requests
import json
import pickle
import concept_mapper_utils as cm
import umls_utils as uu
try:
from umls.umls import UMLSLookup
umls_lu = UMLSLookup()
log.debug('Local py-umls look-up system loaded')
except ImportError:
umls_lu = None
log.debug('Local py-umls look-up system not available')
########################################################################
##
########################################################################
def add_variant_term(auth_client, concepts, cui, variant, head=None):
log.debug('Adding variant term {} ~ {}'.format(cui, variant))
## Make sure we have a CUI entry to hang this variant on
concepts = flesh_out_concept(auth_client, concepts, cui, head=head)
if (cui not in concepts):