Detect Anatomical Structures (BODY_PART)

import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline

val ner_pipeline = PretrainedPipeline("ner_body_part_benchmark_pipeline", "en", "clinical/models")

val text = """HISTORY OF PRESENT ILLNESS :
Mr. He is a 77 year old male with squamous cell carcinoma of the lung .
The initial presentation was the orifice of the right upper lobe with mediastinoscopy positive for subcarinal lymph node .
He received 6,000 rads to his mediastinum with external beam .
Subsequently , he returned to Goo where he received another 3,000 rads via an endobronchial catheter , apparently due to recurrence .
Over the pat three to four weeks , he started having increased dyspnea and noted wheezing .
A bronchoscopy showed protrusion of the tumor into the right main stem bronchus with a positive needle biopsy , washings and brushings for squamous cell carcinoma .
A computerized tomography scan showed a large subcarinal mass .
PAST MEDICAL HISTORY :
His past medical history was significant for malignant bladder tumor in 1991 .
PHYSICAL EXAMINATION :
On physical examination , Mr. He had very marked inspiratory and expiratory stridor .
There were no nodes present .
The breath sounds were somewhat decreased through both lung fields .
His cardiac examination did not show any murmur , gallop , or cardiomegaly .
There was no hepatosplenomegaly , and no peripheral edema .
HOSPITAL COURSE :
A bronchoscopy with the intention of coring out tumor was carried out by Dr. Reg He , but all the tumor was extrinsic to the airway and he was unable to relieve the obstruction .
The tumor now involves the trachea as well as the right main bronchus .
His major complaint was of persistent severe coughing and secretions .
Ultimately , only codeine at 30 mg q6h controlled him and this was very affective .
Inhalers provide only mild relief .
He is aware of his prognosis .
The patient was also seen by Dr. Lenchermoi Fyfesaul of the Oncology Service who did not feel that chemotherapy had anything of promise to offer .
Mr. He is an anxious man , but very pleasant .
He and his family understand his prognosis ."""

val result = ner_pipeline.fullAnnotate(text)