Examples

data ="""The patient is a 5-month-old infant who presented initially on Monday with a cold, cough, and runny nose for 2 days."""
df = nlp.load('med_ner.jsl.wip.clinical en.resolve_chunk.cpt_clinical').predict(data)

# load zero-shot ner model
enterprise_zero_shot_ner = nlp.load('en.zero_shot.ner_roberta')

# Configure entity definitions
enterprise_zero_shot_ner['zero_shot_ner'].setEntityDefinitions(
  {
    "PROBLEM": [
      "What is the disease?",
      "What is his symptom?",
      "What is her disease?",
      "What is his disease?",
      "What is the problem?",
      "What does a patient suffer",
      "What was the reason that the patient is admitted to the clinic?",
    ],
    "DRUG": [
      "Which drug?",
      "Which is the drug?",
      "What is the drug?",
      "Which drug does he use?",
      "Which drug does she use?",
      "Which drug do I use?",
      "Which drug is prescribed for a symptom?",
    ],
    "ADMISSION_DATE": ["When did patient admitted to a clinic?"],
    "PATIENT_AGE": [
      "How old is the patient?",
      "What is the gae of the patient?",
    ],
  }
)

# Predict entities
df = enterprise_zero_shot_ner.predict(
  [
    "The doctor pescribed Majezik for my severe headache.",
    "The patient was admitted to the hospital for his colon cancer.",
    "27 years old patient was admitted to clinic on Sep 1st by Dr."+
    "X for a right-sided pleural effusion for thoracentesis.",
  ]
)
df

data = ["""He has a starvation ketosis but nothing found for significant for dry oral mucosa"""]
nlp.load('med_ner.jsl.wip.clinical resolve.icd10pcs').predict(data)

data = 'MRI demonstrated infarction in the upper brain stem , left cerebellum and  right basil ganglia'
df = nlp.load('en.med_ner.jsl.wip.clinical.greedy en.relation').predict(data)

data = "He has a starvation ketosis but nothing found for significant for dry oral mucosa"
assert_df = nlp.load('en.med_ner.clinical en.assert ').predict(data)

data= 'DR Johnson administerd to the patient Peter Parker last week 30 MG of penicilin on Friday 25. March 1999'
df = nlp.load('de_identify').predict(data)

data = ["Agnogenic one half cup","adalimumab 54.5 + 43.2 gm","aspirin 10 meq/ 5 ml oral sol","interferon alfa-2b 10 million unit ( 1 ml ) injec","Sodium Chloride/Potassium Chloride 13bag"]
nlp.load('norm_drugs').predict(data)

data - ['Covid 19 is']
df = nlu.load('en.text_generator.biomedical_biogpt_base').predict(data)

import nlu
import json
# Define helper functions to write NER rules to file 
"""Generate json with dict contexts at target path"""
def dump_dict_to_json_file(dict, path):
  with open(path, 'w') as f: json.dump(dict, f)

"""Dump raw text file """
def dump_file_to_csv(data,path):
  with open(path, 'w') as f:f.write(data)
sample_text = """A 28-year-old female with a history of gestational diabetes mellitus diagnosed eight years prior to presentation and subsequent type two diabetes mellitus ( T2DM ), one prior episode of HTG-induced pancreatitis three years prior to presentation , associated with an acute hepatitis , and obesity with a body mass index ( BMI ) of 33.5 kg/m2 , presented with a one-week history of polyuria , polydipsia , poor appetite , and vomiting. Two weeks prior to presentation , she was treated with a five-day course of amoxicillin for a respiratory tract infection . She was on metformin , glipizide , and dapagliflozin for T2DM and atorvastatin and gemfibrozil for HTG . She had been on dapagliflozin for six months at the time of presentation . Physical examination on presentation was significant for dry oral mucosa ; significantly , her abdominal examination was benign with no tenderness , guarding , or rigidity . Pertinent laboratory findings on admission were : serum glucose 111 mg/dl , bicarbonate 18 mmol/l , anion gap 20 , creatinine 0.4 mg/dL , triglycerides 508 mg/dL , total cholesterol 122 mg/dL , glycated hemoglobin ( HbA1c ) 10% , and venous pH 7.27 . Serum lipase was normal at 43 U/L . Serum acetone levels could not be assessed as blood samples kept hemolyzing due to significant lipemia . The patient was initially admitted for starvation ketosis , as she reported poor oral intake for three days prior to admission . However , serum chemistry obtained six hours after presentation revealed her glucose was 186 mg/dL , the anion gap was still elevated at 21 , serum bicarbonate was 16 mmol/L , triglyceride level peaked at 2050 mg/dL , and lipase was 52 U/L . β-hydroxybutyrate level was obtained and found to be elevated at 5.29 mmol/L - the original sample was centrifuged and the chylomicron layer removed prior to analysis due to interference from turbidity caused by lipemia again . The patient was treated with an insulin drip for euDKA and HTG with a reduction in the anion gap to 13 and triglycerides to 1400 mg/dL , within 24 hours . Twenty days ago. Her euDKA was thought to be precipitated by her respiratory tract infection in the setting of SGLT2 inhibitor use . At birth the typical boy is growing slightly faster than the typical girl, but the velocities become equal at about seven months, and then the girl grows faster until four years. From then until adolescence no differences in velocity can be detected. 21-02-2020 21/04/2020 """

# Define Gender NER matching rules
gender_rules = {
  "entity": "Gender",
  "ruleScope": "sentence",
  "completeMatchRegex": "true"    }

# Define dict data in csv format
gender_data = '''male,man,male,boy,gentleman,he,him
female,woman,female,girl,lady,old-lady,she,her
neutral,neutral'''

# Dump configs to file 
dump_dict_to_json_file(gender_data, 'gender.csv')
dump_dict_to_json_file(gender_rules, 'gender.json')
gender_NER_pipe = nlp.load('match.context')
gender_NER_pipe.print_info()
gender_NER_pipe['context_matcher'].setJsonPath('gender.json')
gender_NER_pipe['context_matcher'].setDictionary('gender.csv', options={"delimiter":","})
gender_NER_pipe.predict(sample_text)

path = '/path/to/spark_nlp_for_healthcare.json'
nlp.auth(path).load('licensed_model').predict(data)

import nlu
SPARK_NLP_LICENSE           = 'YOUR_SECRETS'
AWS_ACCESS_KEY_ID           = 'YOUR_SECRETS'
AWS_SECRET_ACCESS_KEY       = 'YOUR_SECRETS'
JSL_SECRET                  = 'YOUR_SECRETS'

nlp.auth(SPARK_NLP_LICENSE,AWS_ACCESS_KEY_ID,AWS_SECRET_ACCESS_KEY,JSL_SECRET)