hey @shoaibb, my suggestion would be to use the ner pipeline (see docs 6) to extract the named entities because this is quite tricky to get right.
also, emilyalsentzer/Bio_ClinicalBERT appears to be a pretrained language model so you’ll need to either fine-tune it on a labelled NER dataset or see if you can find an existing model on the Hub that suits your needs. you can find an example on fine-tuning NER models here: Google Colaboratory 5