Pipeline to Resolve Medication Codes

Description

A pretrained resolver pipeline to extract medications and resolve their adverse reactions (ADE), RxNorm, UMLS, NDC, SNOMED CT codes, and action/treatments in clinical text.

Action/treatments are available for branded medication, and SNOMED codes are available for non-branded medication.

This pipeline can be used as Lightpipeline (with annotate/fullAnnotate). You can use medication_resolver_transform_pipeline for Spark transform.

Download Copy S3 URI

How to use

from sparknlp.pretrained import PretrainedPipeline

med_resolver_pipeline = PretrainedPipeline("medication_resolver_pipeline", "en", "clinical/models")

text = """The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet."""

result = med_resolver_pipeline.fullAnnotate(text)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline

val med_resolver_pipeline = new PretrainedPipeline("medication_resolver_pipeline", "en", "clinical/models")

val result = med_resolver_pipeline.fullAnnotate("""The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet.""")
import nlu
nlu.load("en.resolve.medication").predict("""The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera. The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet.""")

Results

|    | chunks                       | entities   | ADE                         |   RxNorm | Action                     | Treatment                                  | UMLS     | SNOMED_CT   | NDC_Product   | NDC_Package   |
|---:|:-----------------------------|:-----------|:----------------------------|---------:|:---------------------------|:-------------------------------------------|:---------|:------------|:--------------|:--------------|
|  0 | Amlodopine Vallarta 10-320mg | DRUG       | Gynaecomastia               |   722131 | NONE                       | NONE                                       | C1949334 | 425838008   | 00093-7693    | 00093-7693-56 |
|  1 | Eviplera                     | DRUG       | Anxiety                     |   217010 | Inhibitory Bone Resorption | Osteoporosis                               | C0720318 | NONE        | NONE          | NONE          |
|  2 | Lescol 40 MG                 | DRUG       | NONE                        |   103919 | Hypocholesterolemic        | Heterozygous Familial Hypercholesterolemia | C0353573 | NONE        | 00078-0234    | 00078-0234-05 |
|  3 | Everolimus 1.5 mg tablet     | DRUG       | Acute myocardial infarction |  2056895 | NONE                       | NONE                                       | C4723581 | NONE        | 00054-0604    | 00054-0604-21 |

Model Information

Model Name: medication_resolver_pipeline
Type: pipeline
Compatibility: Healthcare NLP 4.3.2+
License: Licensed
Edition: Official
Language: en
Size: 3.1 GB

Included Models

  • DocumentAssembler
  • SentenceDetectorDLModel
  • TokenizerModel
  • WordEmbeddingsModel
  • MedicalNerModel
  • NerConverterInternalModel
  • TextMatcherModel
  • ChunkMergeModel
  • ChunkMapperModel
  • ChunkMapperModel
  • ChunkMapperFilterer
  • Chunk2Doc
  • BertSentenceEmbeddings
  • SentenceEntityResolverModel
  • ResolverMerger
  • ResolverMerger
  • ChunkMapperModel
  • ChunkMapperModel
  • ChunkMapperModel
  • ChunkMapperModel
  • ChunkMapperModel
  • ChunkMapperModel
  • Finisher