Description
This pipeline is designed to extract all entities mappable to LOINC codes.
2 NER models are used to achieve this task.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("ner_loinc_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""
A 65-year-old woman presents to the office with generalized fatigue for the last 4 months.
She used to walk 1 mile each evening but now gets tired after 1-2 blocks. She has a history of Crohn disease and hypertension
for which she receives appropriate medications. She is married and lives with her husband. She eats a balanced diet that
includes chicken, fish, pork, fruits, and vegetables. She rarely drinks alcohol and denies tobacco use. Vital signs are
within normal limits. A physical examination is unremarkable. Laboratory studies show the following: Hemoglobin: 9.8g/dL,
Hematocrit: 32%, Mean Corpuscular Volume: 110 μm3.
""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("ner_loinc_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""
A 65-year-old woman presents to the office with generalized fatigue for the last 4 months.
She used to walk 1 mile each evening but now gets tired after 1-2 blocks. She has a history of Crohn disease and hypertension
for which she receives appropriate medications. She is married and lives with her husband. She eats a balanced diet that
includes chicken, fish, pork, fruits, and vegetables. She rarely drinks alcohol and denies tobacco use. Vital signs are
within normal limits. A physical examination is unremarkable. Laboratory studies show the following: Hemoglobin: 9.8g/dL,
Hematocrit: 32%, Mean Corpuscular Volume: 110 μm3.
""")
Results
| | chunks | begin | end | entities |
|---:|:------------------------|--------:|------:|:-----------|
| 0 | Vital signs | 449 | 459 | Test |
| 1 | A physical examination | 489 | 510 | Test |
| 2 | Laboratory studies | 529 | 546 | Test |
| 3 | Hemoglobin | 568 | 577 | Test |
| 4 | Hematocrit | 591 | 600 | Test |
| 5 | Mean Corpuscular Volume | 608 | 630 | Test |
Model Information
| Model Name: | ner_loinc_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