SNOMED ChunkResolver

...

snomed_resolver = ChunkEntityResolverModel.pretrained("chunkresolve_snomed_findings_clinical","en","clinical/models")\
	.setInputCols("token","chunk_embeddings")\
	.setOutputCol("snomed_resolution")
    
pipeline_snomed = Pipeline(stages = [documentAssembler, sentenceDetector, tokenizer, stopwords, word_embeddings, clinical_ner, snomed_ner_converter, chunk_embeddings, snomed_resolver])

data = ["""Pentamidine 300 mg IV q . 36 hours , Pentamidine nasal wash 60 mg per 6 ml of sterile water q.d . , voriconazole 200 mg p.o . b.i.d . , acyclovir 400 mg p.o . b.i.d . , cyclosporine 50 mg p.o . b.i.d . , prednisone 60 mg p.o . q.d . , GCSF 480 mcg IV q.d . , Epogen 40,000 units subcu q . week , Protonix 40 mg q.d . , Simethicone 80 mg p.o . q . 8 , nitroglycerin paste 1 " ; q . 4 h . p.r.n . , flunisolide nasal inhaler , 2 puffs q . 8 , OxyCodone 10-15 mg p.o . q . 6 p.r.n . , Sudafed 30 mg q . 6 p.o . p.r.n . , Fluconazole 2% cream b.i.d . to erythematous skin lesions , Ditropan 5 mg p.o . b.i.d . , Tylenol 650 mg p.o . q . 4 h . p.r.n . , Ambien 5-10 mg p.o . q . h.s . p.r.n . , Neurontin 100 mg q . a.m . , 200 mg q . p.m . , Aquaphor cream b.i.d . p.r.n . , Lotrimin 1% cream b.i.d . to feet , Dulcolax 5-10 mg p.o . q.d . p.r.n . , Phoslo 667 mg p.o . t.i.d . , Peridex 0.12% , 15 ml p.o . b.i.d . mouthwash , Benadryl 25-50 mg q . 4-6 h . p.r.n . pruritus , Sarna cream q.d . p.r.n . pruritus , Nystatin 5 ml p.o . q.i.d . swish and !""",

"""Albuterol nebulizers 2.5 mg q.4h . and Atrovent nebulizers 0.5 mg q.4h . , please alternate albuterol and Atrovent ; Rocaltrol 0.25 mcg per NG tube q.d .; calcium carbonate 1250 mg per NG tube q.i.d .; vitamin B12 1000 mcg IM q . month , next dose is due Nov 18 ; diltiazem 60 mg per NG tube t.i.d .; ferrous sulfate 300 mg per NG t.i.d .; Haldol 5 mg IV q.h.s .; hydralazine 10 mg IV q.6h . p.r.n . hypertension ; lisinopril 10 mg per NG tube q.d .; Ativan 1 mg per NG tube q.h.s .; Lopressor 25 mg per NG tube t.i.d .; Zantac 150 mg per NG tube b.i.d .; multivitamin 10 ml per NG tube q.d .; Macrodantin 100 mg per NG tube q.i.d . x 10 days beginning on 11/3/00 .""",

"""Tylenol 650 mg p.o . q . 4-6h p.r.n . headache or pain ; acyclovir 400 mg p.o . t.i.d .; acyclovir topical t.i.d . to be applied to lesion on corner of mouth ; Peridex 15 ml p.o . b.i.d .; Mycelex 1 troche p.o . t.i.d .; g-csf 404 mcg subcu q.d .; folic acid 1 mg p.o . q.d .; lorazepam 1-2 mg p.o . q . 4-6h p.r.n . nausea and vomiting ; Miracle Cream topical q.d . p.r.n . perianal irritation ; Eucerin Cream topical b.i.d .; Zantac 150 mg p.o . b.i.d .; Restoril 15-30 mg p.o . q . h.s . p.r.n . insomnia ; multivitamin 1 tablet p.o . q.d .; viscous lidocaine 15 ml p.o . q . 3h can be applied to corner of mouth or lips p.r.n . pain control ."""]

model = pipeline_snomed.fit(spark.createDataFrame([['']]).toDF("text"))

results = model.transform(spark.createDataFrame(pd.DataFrame({"text": data})))