Description
This pipeline is designed to extract all entities mappable to SNOMED Concept codes.
2 NER models are used to achieve those tasks.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("ner_snomed_auxConcepts_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""
This is an 82-year-old male with a history of prior tobacco use, hypertension, chronic renal insufficiency, COPD, gastritis, and TIA.
He initially presented to Braintree with a nonspecific ST-T abnormality and was transferred to St. Margaret’s Center.
He underwent cardiac catheterization because of occlusion of the mid left anterior descending coronary artery lesion, which was complicated by hypotension and bradycardia.
He required atropine, IV fluids, and dopamine, possibly secondary to a vagal reaction.
""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("ner_snomed_auxConcepts_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""
This is an 82-year-old male with a history of prior tobacco use, hypertension, chronic renal insufficiency, COPD, gastritis, and TIA.
He initially presented to Braintree with a nonspecific ST-T abnormality and was transferred to St. Margaret’s Center.
He underwent cardiac catheterization because of occlusion of the mid left anterior descending coronary artery lesion, which was complicated by hypotension and bradycardia.
He required atropine, IV fluids, and dopamine, possibly secondary to a vagal reaction.
""")
Results
| | chunks | begin | end | entities |
|---:|:------------------------|--------:|------:|:----------------|
| 0 | tobacco | 53 | 59 | Smoking |
| 1 | nonspecific | 179 | 189 | Modifier |
| 2 | cardiac catheterization | 268 | 290 | Procedure |
| 3 | atropine | 440 | 447 | Drug_Ingredient |
| 4 | IV fluids | 450 | 458 | TREATMENT |
| 5 | dopamine | 465 | 472 | Drug_Ingredient |
Model Information
| Model Name: | ner_snomed_auxConcepts_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
- NerConverter
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- ChunkMergeModel