Description
This pipeline is designed to extract all entities mappable to HPO codes.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("ner_hpo_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""She is followed by Dr. X in our office and has a history of severe tricuspid regurgitation.
On 05/12/08, preserved left and right ventricular systolic function, aortic sclerosis with apparent mild aortic stenosis.
She has previously had a Persantine Myoview nuclear rest-stress test scan completed at ABCD Medical Center in 07/06 that was negative.
She has had significant mitral valve regurgitation in the past being moderate, but on the most recent echocardiogram on 05/12/08, that was not felt to be significant.
She does have a history of significant hypertension in the past. She has had dizzy spells and denies clearly any true syncope.
She has had bradycardia in the past from beta-blocker therapy.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("ner_hpo_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""She is followed by Dr. X in our office and has a history of severe tricuspid regurgitation.
On 05/12/08, preserved left and right ventricular systolic function, aortic sclerosis with apparent mild aortic stenosis.
She has previously had a Persantine Myoview nuclear rest-stress test scan completed at ABCD Medical Center in 07/06 that was negative.
She has had significant mitral valve regurgitation in the past being moderate, but on the most recent echocardiogram on 05/12/08, that was not felt to be significant.
She does have a history of significant hypertension in the past. She has had dizzy spells and denies clearly any true syncope.
She has had bradycardia in the past from beta-blocker therapy.""")
Results
| | chunks | begin | end | entities |
|---:|:---------------------------|--------:|------:|:-----------|
| 0 | tricuspid regurgitation | 68 | 90 | HP |
| 1 | aortic stenosis | 199 | 213 | HP |
| 2 | mitral valve regurgitation | 377 | 402 | HP |
| 3 | hypertension | 560 | 571 | HP |
| 4 | bradycardia | 661 | 671 | HP |
Model Information
| Model Name: | ner_hpo_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 6.0.2+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.7 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel