Description
This pipeline is designed to extract all entities mappable to SNOMED (Findings and Concepts) codes.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("ner_snomed_auxConcepts_findings_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, chronic obstructive pulmonary disease, gastritis, and transient ischemic attack.
He initially presented to Braintree with ST elevation and was transferred to St. Margaret’s Center.
He underwent cardiac catheterization because of the left main coronary artery stenosis, which was complicated by hypotension and bradycardia.
He required atropine, IV fluids, and dopamine. He was subsequently transferred to the CCU for close monitoring
""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("ner_snomed_auxConcepts_findings_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, chronic obstructive pulmonary disease, gastritis, and transient ischemic attack.
He initially presented to Braintree with ST elevation and was transferred to St. Margaret’s Center.
He underwent cardiac catheterization because of the left main coronary artery stenosis, which was complicated by hypotension and bradycardia.
He required atropine, IV fluids, and dopamine. He was subsequently transferred to the CCU for close monitoring
""")
Results
| | chunks | begin | end | entities |
|---:|:---------------------------------------|--------:|------:|:--------------------------|
| 0 | tobacco | 53 | 59 | Smoking |
| 1 | hypertension | 66 | 77 | Hypertension |
| 2 | chronic renal insufficiency | 80 | 106 | Kidney_Disease |
| 3 | chronic obstructive pulmonary disease | 109 | 145 | Disease_Syndrome_Disorder |
| 4 | gastritis | 148 | 156 | Disease_Syndrome_Disorder |
| 5 | transient ischemic attack | 163 | 187 | Cerebrovascular_Disease |
| 6 | ST elevation | 232 | 243 | snomed_term |
| 7 | cardiac catheterization | 305 | 327 | Procedure |
| 8 | the left main coronary artery stenosis | 340 | 377 | PROBLEM |
| 9 | hypotension | 405 | 415 | VS_Finding |
| 10 | bradycardia | 421 | 431 | VS_Finding |
| 11 | atropine | 447 | 454 | Drug_Ingredient |
| 12 | IV fluids | 457 | 465 | TREATMENT |
| 13 | dopamine | 472 | 479 | Drug_Ingredient |
Model Information
| Model Name: | ner_snomed_auxConcepts_findings_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 6.0.2+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.8 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- ChunkMergeModel