Description
This pretrained pipeline is built on the top of ner_eu_clinical_case model.
How to use
from sparknlp.pretrained import PretrainedPipeline
pipeline = PretrainedPipeline("ner_eu_clinical_case_pipeline", "en", "clinical/models")
text = "
A 3-year-old boy with autistic disorder on hospital of pediatric ward A at university hospital. He has no family history of illness or autistic spectrum disorder. The child was diagnosed with a severe communication disorder, with social interaction difficulties and sensory processing delay. Blood work was normal (thyroid-stimulating hormone (TSH), hemoglobin, mean corpuscular volume (MCV), and ferritin). Upper endoscopy also showed a submucosal tumor causing subtotal obstruction of the gastric outlet. Because a gastrointestinal stromal tumor was suspected, distal gastrectomy was performed. Histopathological examination revealed spindle cell proliferation in the submucosal layer.
"
result = pipeline.fullAnnotate(text)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val pipeline = new PretrainedPipeline("ner_eu_clinical_case_pipeline", "en", "clinical/models")
val text = "
A 3-year-old boy with autistic disorder on hospital of pediatric ward A at university hospital. He has no family history of illness or autistic spectrum disorder. The child was diagnosed with a severe communication disorder, with social interaction difficulties and sensory processing delay. Blood work was normal (thyroid-stimulating hormone (TSH), hemoglobin, mean corpuscular volume (MCV), and ferritin). Upper endoscopy also showed a submucosal tumor causing subtotal obstruction of the gastric outlet. Because a gastrointestinal stromal tumor was suspected, distal gastrectomy was performed. Histopathological examination revealed spindle cell proliferation in the submucosal layer.
"
val result = pipeline.fullAnnotate(text)
Results
| | chunks | begin | end | entities | confidence |
|---:|:-------------------------------|--------:|------:|:-------------------|-------------:|
| 0 | A 3-year-old boy | 1 | 16 | patient | 0.733133 |
| 1 | autistic disorder | 23 | 39 | clinical_condition | 0.5412 |
| 2 | He | 97 | 98 | patient | 0.9991 |
| 3 | illness | 125 | 131 | clinical_event | 0.4956 |
| 4 | autistic spectrum disorder | 136 | 161 | clinical_condition | 0.5002 |
| 5 | The child | 164 | 172 | patient | 0.82435 |
| 6 | diagnosed | 178 | 186 | clinical_event | 0.9912 |
| 7 | disorder | 216 | 223 | clinical_event | 0.3804 |
| 8 | difficulties | 250 | 261 | clinical_event | 0.3221 |
| 9 | Blood | 293 | 297 | bodypart | 0.7617 |
| 10 | work | 299 | 302 | clinical_event | 0.9361 |
| 11 | normal | 308 | 313 | units_measurements | 0.5337 |
| 12 | hormone | 336 | 342 | clinical_event | 0.362 |
| 13 | hemoglobin | 351 | 360 | clinical_event | 0.6106 |
| 14 | volume | 380 | 385 | clinical_event | 0.6226 |
| 15 | endoscopy | 415 | 423 | clinical_event | 0.9917 |
| 16 | showed | 430 | 435 | clinical_event | 0.9904 |
| 17 | tumor | 450 | 454 | clinical_condition | 0.5606 |
| 18 | causing | 456 | 462 | clinical_event | 0.7362 |
| 19 | obstruction | 473 | 483 | clinical_event | 0.6198 |
| 20 | the gastric outlet | 488 | 505 | bodypart | 0.634967 |
| 21 | gastrointestinal stromal tumor | 518 | 547 | clinical_condition | 0.387833 |
| 22 | suspected | 553 | 561 | clinical_event | 0.8225 |
| 23 | gastrectomy | 571 | 581 | clinical_event | 0.935 |
| 24 | examination | 616 | 626 | clinical_event | 0.9987 |
| 25 | revealed | 628 | 635 | clinical_event | 0.9989 |
| 26 | spindle cell proliferation | 637 | 662 | clinical_condition | 0.4487 |
| 27 | the submucosal layer | 667 | 686 | bodypart | 0.523 |
Model Information
| Model Name: | ner_eu_clinical_case_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 4.3.0+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.7 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel