Sentence Entity Resolver for SNOMED CT (Drugs) (sbiobert_base_cased_mli_onnx embeddings) - Pipeline

Description

This pipeline extracts clinical entities from text and maps them to SNOMED CT drug/substance concepts using sbiobert_base_cased_mli_onnx embeddings. Wraps the sbiobertresolve_snomed_drug_20260901 resolver, trained on SNOMED CT US Edition 20260901.

Live Demo Open in Colab Copy S3 URI

How to use


from sparknlp.pretrained import PretrainedPipeline

snomed_pipeline = PretrainedPipeline("sbiobertresolve_snomed_drug_pipeline_20260901", "en", "clinical/models")

data = spark.createDataFrame([["John's doctor prescribed aspirin for his heart condition, along with paracetamol for his fever and headache, amoxicillin for his tonsilitis and lansoprazole for his GORD."]]).toDF("text")
result = snomed_pipeline.transform(data)


from johnsnowlabs import nlp, medical

snomed_pipeline = nlp.PretrainedPipeline("sbiobertresolve_snomed_drug_pipeline_20260901", "en", "clinical/models")

data = spark.createDataFrame([["John's doctor prescribed aspirin for his heart condition, along with paracetamol for his fever and headache, amoxicillin for his tonsilitis and lansoprazole for his GORD."]]).toDF("text")
result = snomed_pipeline.transform(data)


import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline

val snomed_pipeline = PretrainedPipeline("sbiobertresolve_snomed_drug_pipeline_20260901", "en", "clinical/models")

val data = Seq("John's doctor prescribed aspirin for his heart condition, along with paracetamol for his fever and headache, amoxicillin for his tonsilitis and lansoprazole for his GORD.").toDF("text")
val result = snomed_pipeline.transform(data)

Results

| chunk        | label   |   snomed_code | resolution   | all_codes                                                                                                                                                                                                                                                                                | all_resolutions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
|:-------------|:--------|--------------:|:-------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| aspirin      | DRUG    |     387458008 | aspirin      | 387458008:::7947003:::426365001:::412566001:::25796002:::87303007:::319796006:::398767009:::785413006:::358427004:::735135008:::51622009:::9913005:::373444002:::424039006:::398649009:::370337008:::259699009:::398683002:::130699009:::713473008                                       | aspirin:::aspirin-containing product:::aspirin, buffered:::buffered aspirin-containing product:::aluminium aspirin:::cephapirin:::aspirin- and dipyridamole-containing product:::aspirin- and glycine-containing product:::aspirin-containing product in oromucosal dose form:::aspirin-containing product in oral dose form:::aspirin dl-lysine:::adenase:::arachidic acid:::atorvastatin:::peroxyacetic acid-containing product:::aspirin- and carisoprodol-containing product:::cephapirin-containing product:::antianemia agent:::aspirin- and meprobamate-containing product:::astacin:::spirapril                                  |
| paracetamol  | DRUG    |     387517004 | paracetamol  | 387517004:::1285524005:::90332006:::395833008:::18712002:::724182003:::59034000:::417551008:::391704009:::387201009:::423801005:::398663003:::412499001:::322998004:::398826009:::398918002:::1285523004:::35281007:::86223002:::372699006:::423936008:::96251009:::39815009:::763002008 | paracetamol:::propacetamol:::paracetamol-containing product:::piracetam:::phenacemide:::paracetamol crystal:::trometamol:::acetamide:::acemetacin:::phenindamine:::isometheptene- and paracetamol-containing product:::paracetamol- and salicylamide-containing product:::paracetamol- and pseudoephedrine-containing product:::piracetam-containing product:::butalbital- and paracetamol-containing product:::methionine- and paracetamol-containing product:::propacetamol hydrochloride:::acetophenazine:::protaminase:::pentamidine:::diphenhydramine- and paracetamol-containing product:::crotetamide:::clorazepate:::carfentanil |
| amoxicillin  | DRUG    |     372687004 | amoxicillin  | 372687004:::27658006:::427483001:::117147001:::387170002:::373276005:::442859000:::373298001:::372873001:::387544009:::372786004:::387266001:::31087008:::373515001:::372868007:::785686003:::96068000:::43048003:::41332001:::373274008:::387543003:::82885001:::412439003:::58883005   | amoxicillin:::amoxicillin-containing product:::amoxicillin sodium:::almecillin:::ampicillin:::cloxacillin:::amifloxacin:::aminopenicillin:::dicloxacillin:::flucloxacillin:::clindamycin:::amikacin:::ampicillin-containing product:::meticillin:::oxacillin:::amoxicillin anhydrous:::amoxicillin trihydrate:::amfomycin:::amimycin:::acylaminopenicillin:::temocillin:::colistimethate:::moxifloxacin:::clindamycin-containing product                                                                                                                                                                                                 |
| lansoprazole | DRUG    |     386888004 | lansoprazole | 386888004:::108666007:::441863009:::716069007:::372549002:::395774003:::396047003:::387137007:::422225001:::785533007:::387325003:::715182007:::395978007:::387562000:::96102004:::363554004:::442011001:::395772004:::55944008:::317331009:::96126002:::386983007:::116087001           | lansoprazole:::lansoprazole-containing product:::dexlansoprazole:::brexpiprazole:::dapiprazole:::loprazolam:::esomeprazole:::omeprazole:::rabeprazole:::lansoprazole-containing product in oromucosal dose form:::clotrimazole:::aripiprazole lauroxil:::clomethiazole:::lamotrigine:::carnidazole:::tolazoline:::loprazolam mesylate:::lofepramine:::niridazole:::esomeprazole-containing product:::cambendazole:::alprazolam:::cilostazol                                                                                                                                                                                              |

Model Information

Model Name: sbiobertresolve_snomed_drug_pipeline_20260901
Type: pipeline
Compatibility: Healthcare NLP 6.4.1+
License: Licensed
Edition: Official
Language: en
Size: 2.4 GB

Included Models

  • DocumentAssembler
  • SentenceDetectorDLModel
  • TokenizerModel
  • WordEmbeddingsModel
  • MedicalNerModel
  • NerConverterInternalModel
  • Chunk2Doc
  • BertSentenceEmbeddings
  • SentenceEntityResolverModel