Description
This pipeline is designed to extract all entities mappable to SNOMED (Procedures and Measurements) codes.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("ner_snomed_procedures_measurements_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""
Based on the severity of her abdominal examination and the persistence of her symptoms,
it has been determined that she requires a laparoscopic jejunectomy, possible appendectomy, and
cholecystectomy.Laboratory values indicate a white blood cell count of 15.3,
hemoglobin level of 12.8, and normal platelet count. Alkaline phosphatase is elevated at 184,
while liver function tests are otherwise normal. Electrolyte levels are within the normal range.
Glucose levels are at 134, BUN is 4, and creatinine is 0.7.
""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("ner_snomed_procedures_measurements_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""
Based on the severity of her abdominal examination and the persistence of her symptoms,
it has been determined that she requires a laparoscopic jejunectomy, possible appendectomy, and
cholecystectomy.Laboratory values indicate a white blood cell count of 15.3,
hemoglobin level of 12.8, and normal platelet count. Alkaline phosphatase is elevated at 184,
while liver function tests are otherwise normal. Electrolyte levels are within the normal range.
Glucose levels are at 134, BUN is 4, and creatinine is 0.7.
""")
Results
| | chunks | begin | end | entities |
|---:|:-------------------------|--------:|------:|:-----------|
| 0 | laparoscopic jejunectomy | 144 | 167 | Procedure |
| 1 | appendectomy | 179 | 190 | Procedure |
| 2 | cholecystectomy | 209 | 223 | Procedure |
| 3 | white blood cell count | 254 | 275 | Test |
| 4 | hemoglobin level | 298 | 313 | Test |
| 5 | platelet count | 335 | 348 | Test |
| 6 | Alkaline phosphatase | 351 | 370 | Test |
| 7 | liver function tests | 410 | 429 | Test |
| 8 | Electrolyte levels | 453 | 470 | Test |
| 9 | Glucose levels | 513 | 526 | Test |
| 10 | BUN | 540 | 542 | Test |
| 11 | creatinine | 554 | 563 | Test |
Model Information
| Model Name: | ner_snomed_procedures_measurements_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