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
Cerebrovascular_Disease, Communicable_Disease, DRUG, DRUGG, Diabetes, Disease_Syndrome_Disorder, EKG_Findings, Heart_Disease, Hyperlipidemia, Hypertension, ImagingFindings, Injury_or_Poisoning, Kidney_Disease, Obesity, Oncological, Overweight, PROBLEM, Pregnancy, Psychological_Condition, Symptom, VS_Finding
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 upper quadrant pain radiating to her back starting yesterday.
She has a history of infective pericarditis and gestational diabetes mellitus in May 2006.
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 result = resolver_pipeline.annotate("""The patient is a 41-year-old Vietnamese female with a cough that started last week.
She has had right upper quadrant pain radiating to her back starting yesterday.
She has a history of infective pericarditis and gestational diabetes mellitus in May 2006.
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
+-------+----------------------+------+-----------+-----------+-------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------+
|sent_id| ner_chunk|entity|rxnorm_code| resolution| all_codes| resolutions|
+-------+----------------------+------+-----------+-----------+-------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------+
| 5| Coumadin 1 mg| DRUG| 855289| coumadin | 855289:::438737:::208469:::205489:::447086:::205485...| warfarin sodium 1 MG [Coumadin]:::coumarin 1 MG[coumarin 1 MG]:::terazosin 1 MG Oral Capsule [Hytrin]...|
| 6| Amiodarone 100 mg p.o| DRUG| 835956|amiodarone | 835956:::835955:::876015:::565346:::875937:::440437...|amiodarone hydrochloride 100 MG Oral Tablet:::amiodarone hydrochloride 100 MG[amiodarone hydrochloride 100 MG]...|
+-------+----------------------+------+-----------+-----------+-------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------+
# ICD-10-CM RESULT
+-------+-----------------------------+-------+------------+------------------------------+------------------------------------------------------------+------------------------------------------------------------+------------------------------------------------------------+
|sent_id| ner_chunk| entity|icd10cm_code| resolution| all_codes| resolutions| hcc_list|
+-------+-----------------------------+-------+------------+------------------------------+------------------------------------------------------------+------------------------------------------------------------+------------------------------------------------------------+
| 0| a cough|PROBLEM| R05| cough |R05:::R05.3:::R05.1:::A37:::R05.2:::R06.01:::R06.7:::R06....|cough [cough]:::chronic cough [chronic cough]:::acute cou...|0||0||0:::1||0||0:::1||0||0:::0||0||0:::1||0||0:::1||0||0...|
| 1| right upper quadrant pain|PROBLEM| R10.11| right upper quadrant pain |R10.11:::M79.621:::R10.31:::M79.651:::M79.631:::M79.601::...|right upper quadrant pain [right upper quadrant pain]:::p...|1||0||0:::1||0||0:::1||0||0:::1||0||0:::1||0||0:::1||0||0...|
| 2| infective pericarditis|PROBLEM| I30.1| infective pericarditis |I30.1:::I30:::I31.0:::B33.23:::I01.0:::I30.0:::I31.1:::A3...|infective pericarditis [infective pericarditis]:::acute p...|1||0||0:::0||0||0:::1||0||0:::1||0||0:::1||0||0:::1||0||0...|
| 2|gestational diabetes mellitus|PROBLEM| O24.4|gestational diabetes mellitus |O24.4:::O24.41:::Z86.32:::O24.11:::O24.81:::P70.2:::O24.0...|gestational diabetes mellitus [gestational diabetes melli...|0||0||0:::0||0||0:::1||0||0:::0||0||0:::0||0||0:::1||0||0...|
+-------+-----------------------------+-------+------------+------------------------------+------------------------------------------------------------+------------------------------------------------------------+------------------------------------------------------------+
Model Information
| Model Name: | icd10cm_rxnorm_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.4.0+ |
| 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