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_term_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""
The patient was diagnosed with acute appendicitis and scheduled for immediate surgery.",
"Due to experiencing chronic pain the patient was referred to a fibromyalgia specialist for further evaluation.",
"His hypertension is currently managed with a combination of lifestyle modifications and medication.",
"The child was brought in with symptoms of acute otitis including ear pain and fever.",
"Laboratory tests indicate the individual has hyperthyroidism requiring further endocrinological assessment.",
"The radiograph showed evidence of a distal radius fracture from a recent fall.
""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("ner_snomed_term_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""
The patient was diagnosed with acute appendicitis and scheduled for immediate surgery.",
"Due to experiencing chronic pain the patient was referred to a fibromyalgia specialist for further evaluation.",
"His hypertension is currently managed with a combination of lifestyle modifications and medication.",
"The child was brought in with symptoms of acute otitis including ear pain and fever.",
"Laboratory tests indicate the individual has hyperthyroidism requiring further endocrinological assessment.",
"The radiograph showed evidence of a distal radius fracture from a recent fall.
""")
Results
| | chunks | begin | end | entities |
|---:|:-----------------------|--------:|------:|:------------|
| 0 | acute appendicitis | 32 | 49 | snomed_term |
| 1 | chronic pain | 111 | 122 | snomed_term |
| 2 | fibromyalgia | 154 | 165 | snomed_term |
| 3 | hypertension | 209 | 220 | snomed_term |
| 4 | otitis | 356 | 361 | snomed_term |
| 5 | ear pain | 373 | 380 | snomed_term |
| 6 | fever | 386 | 390 | snomed_term |
| 7 | hyperthyroidism | 441 | 455 | snomed_term |
| 8 | radiograph | 511 | 520 | snomed_term |
| 9 | distal radius fracture | 543 | 564 | snomed_term |
Model Information
| Model Name: | ner_snomed_term_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