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.

Predicated Entities

RxNorm Code UMLS Code NDC Code SNOMED CT codes

Predicted Entities

DRUG

Open in Colab Copy S3 URI

How to use

from sparknlp.pretrained import PretrainedPipeline

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

result = resolver_pipeline.annotate("""The patient was prescribed Amlodopine Vallarta 10-320mg, Eviplera.
The other patient is given Lescol 40 MG and Everolimus 1.5 mg tablet.
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline

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

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

Results

+----------------------------+---------+---------------------------+-------+--------------------------+------------------------------------------+--------+---------+-----------+-------------+
|chunk                       |ner_label|ADE                        |RxNorm |Action                    |Treatment                                 |UMLS    |SNOMED_CT|NDC_Product|NDC_Package  |
+----------------------------+---------+---------------------------+-------+--------------------------+------------------------------------------+--------+---------+-----------+-------------+
|Amlodopine Vallarta 10-320mg|DRUG     |Gynaecomastia              |722131 |NONE                      |NONE                                      |C1949334|425838008|00093-7693 |00093-7693-56|
|Eviplera                    |DRUG     |Anxiety                    |217010 |Inhibitory Bone Resorption|Osteoporosis                              |C0720318|NONE     |NONE       |NONE         |
|Lescol 40 MG                |DRUG     |NONE                       |103919 |Hypocholesterolemic       |Heterozygous Familial Hypercholesterolemia|C0353573|NONE     |00078-0234 |00078-0234-05|
|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 5.4.1+
License: Licensed
Edition: Official
Language: en
Size: 3.3 GB

Included Models

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