Description
This pipeline is designed to extract all entities mappable to MedDRA PT (Preferred Term) codes.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("ner_meddra_pt_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""This is an 82-year-old male with a history of prior tobacco use, benign hypertension, chronic renal insufficiency, chronic bronchitis, gastritis, and 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.
We describe the side effects of 5-FU in a colon cancer patient who suffered mucositis and dermatitis.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("ner_meddra_pt_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""This is an 82-year-old male with a history of prior tobacco use, benign hypertension, chronic renal insufficiency, chronic bronchitis, gastritis, and 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.
We describe the side effects of 5-FU in a colon cancer patient who suffered mucositis and dermatitis.""")
Results
| | chunks | begin | end | entities |
|---:|:---------------------------------------|--------:|------:|:--------------------------|
| 0 | tobacco | 53 | 59 | Smoking |
| 1 | benign hypertension | 66 | 84 | PROBLEM |
| 2 | chronic renal insufficiency | 87 | 113 | Kidney_Disease |
| 3 | chronic bronchitis | 116 | 133 | PROBLEM |
| 4 | gastritis | 136 | 144 | Disease_Syndrome_Disorder |
| 5 | ischemic attack | 151 | 165 | Cerebrovascular_Disease |
| 6 | ST elevation | 210 | 221 | PROBLEM |
| 7 | cardiac catheterization | 283 | 305 | Procedure |
| 8 | the left main coronary artery stenosis | 318 | 355 | PROBLEM |
| 9 | hypotension | 383 | 393 | VS_Finding |
| 10 | bradycardia | 399 | 409 | VS_Finding |
| 11 | the side effects | 425 | 440 | PROBLEM |
| 12 | a colon cancer | 453 | 466 | PROBLEM |
| 13 | mucositis | 489 | 497 | Disease_Syndrome_Disorder |
| 14 | dermatitis | 503 | 512 | Disease_Syndrome_Disorder |
Model Information
| Model Name: | ner_meddra_pt_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
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel