Description
This pipeline can extract clinical conditions and medication entities, map the clinical conditions to their respective ICD-10-CM codes, and medication entities to RxNorm codes using sbiobert_base_cased_mli Sentence Bert Embeddings. Users can refer to the following entity labels for pertinent concepts:
- ICD-10-CM entities: PROBLEM, CEREBROVASCULAR_DISEASE, COMMUNICABLE_DISEASE, DIABETES, DISEASE_SYNDROME_DISORDER, EKG_FINDINGS, HEART_DISEASE, HYPERLIPIDEMIA, HYPERTENSION, IMAGINGFINDINGS, INJURY_OR_POISONING, KIDNEY_DISEASE, OBESITY, ONCOLOGICAL, OVERWEIGHT, PREGNANCY, PSYCHOLOGICAL_CONDITION, SYMPTOM, VS_FINDING
- RxNorm entities: DRUG
Predicted Entities
ICD-10-CM Code Rxnorm Code
How to use
from sparknlp.pretrained import PretrainedPipeline
resolver_pipeline = PretrainedPipeline("icd10cm_rxnorm_resolver_pipeline", "en", "clinical/models")
result = resolver_pipeline.annotate("""The patient is a 41-year-old Vietnamese female with a cough that started last week.
She has had right-sided chest pain radiating to her back with fever starting yesterday.
She has a history of pericarditis in May 2006 and developed cough with right-sided chest pain.
MEDICATIONS
1. Coumadin 1 mg daily. Last INR was on Tuesday, August 14, 2007, and her INR was 2.3.
2. Amiodarone 100 mg p.o. daily.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val resolver_pipeline = PretrainedPipeline("icd10cm_rxnorm_resolver_pipeline", "en", "clinical/models")
val result = resolver_pipeline.annotate("""The patient is a 41-year-old Vietnamese female with a cough that started last week.
She has had right-sided chest pain radiating to her back with fever starting yesterday.
She has a history of pericarditis in May 2006 and developed cough with right-sided chest pain.
MEDICATIONS
1. Coumadin 1 mg daily. Last INR was on Tuesday, August 14, 2007, and her INR was 2.3.
2. Amiodarone 100 mg p.o. daily.""")
Results
# RXNORM RESULT
| chunks | begin | end | code | all_codes | resolutions |
| ------------- | ----- | --- | ------ | --------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Coumadin 1 mg | 282 | 294 | 855289 | [855289, 438737, 208469, 205489, 447086, 205485... | [warfarin sodium 1 MG [Coumadin], coumarin 1 MG[coumarin 1 MG], terazosin 1 MG Oral Capsule [Hytrin], bumetanide 1 MG Oral Tablet [Bumex], propinox 1 MG[propinox 1 MG], dextrothyroxine 1 MG Oral Tablet [Choloxin]... |
| Amiodarone | 369 | 378 | 703 | [703, 1663223, 1151983, 1663270, 1151982, 203114... | [amiodarone[amiodarone], amiodarone Injection[amiodarone Injection], amiodarone Pill[amiodarone Pill], amiodarone Injection [Nexterone][amiodarone Injection [Nexterone]], amiodarone Oral Product[amiodarone Oral Product], amiodarone hydrochloride[amiodarone hydrochloride]... |
# ICD-10-CM RESULT
| chunks | begin | end | code | all_codes | resolutions |
|------------------------|-------|-----|--------|----------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| a cough | 52 | 58 | R05 | [R05, R05.3, R05.1, A37, R05.2, R06.01...] | [cough, chronic cough, acute cough, whooping cough, subacute cough, orthopnea...] |
| right-sided chest pain | 96 | 117 | R10.11 | [R10.11, M79.621, M79.604, M79.601, M25.511, M79.631...] | [right upper quadrant pain, pain in right upper arm, pain in right leg, pain in right arm, pain in right shoulder, pain in right forearm...] |
| fever | 146 | 150 | A68 | [A68, A78, R50.2, M04.1, A96.2, A68.9...] | [relapsing fevers, q fever, drug induced fever, periodic fever syndromes, lassa fever, relapsing fever, unspecified...] |
| pericarditis | 193 | 204 | I30.1 | [I30.1, B33.23, I30, I31.0, I01.0, I30.9...] | [infective pericarditis, viral pericarditis, acute pericarditis, chronic adhesive pericarditis, acute rheumatic pericarditis, acute pericarditis, unspecified...] |
| cough | 232 | 236 | R05 | [R05, A37, R05.3, R05.1, R05.2, R06.7...] | [cough, whooping cough, chronic cough, acute cough, subacute cough, sneezing...] |
| right-sided chest pain | 243 | 264 | R10.11 | [R10.11, M79.621, M79.604, M79.601, M25.511, M79.631...] | [right upper quadrant pain, pain in right upper arm, pain in right leg, pain in right arm, pain in right shoulder, pain in right forearm...] |
Model Information
| Model Name: | icd10cm_rxnorm_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.4.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 3.7 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- TextMatcherInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- ChunkMergeModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- Router
- Router
- SentenceEntityResolverModel
- SentenceEntityResolverModel