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,TEST,TREATMENT,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, 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 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 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| DRUG| 202421| coumadin |202421:::2898:::374998:::1855075:::128793:::1598:::152085...|coumadin [coumadin]:::coumarin [coumarin]:::coumarin Oral...|
| 6|Amiodarone| DRUG| 703|amiodarone |703:::1663223:::1151983:::1663270:::1151982:::203114:::37...|amiodarone [amiodarone]:::amiodarone Injection:::amiodaro...|
+-------+----------+------+-----------+-----------+------------------------------------------------------------+------------------------------------------------------------+
# 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 5.3.0+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 3.8 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- TextMatcherInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- ChunkMergeModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- Router
- Router
- SentenceEntityResolverModel
- SentenceEntityResolverModel