Description
This pipeline extracts clinical entities from text and maps them to SNOMED CT procedure and measurement concepts using sbiobert_base_cased_mli_onnx embeddings. Wraps the sbiobertresolve_snomed_procedures_measurements_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_procedures_measurements_pipeline_20260901", "en", "clinical/models")
data = spark.createDataFrame([["The patient underwent a laparoscopic cholecystectomy and appendectomy. Laboratory testing showed an elevated white blood cell count."]]).toDF("text")
result = snomed_pipeline.transform(data)
from johnsnowlabs import nlp, medical
snomed_pipeline = nlp.PretrainedPipeline("sbiobertresolve_snomed_procedures_measurements_pipeline_20260901", "en", "clinical/models")
data = spark.createDataFrame([["The patient underwent a laparoscopic cholecystectomy and appendectomy. Laboratory testing showed an elevated white blood cell count."]]).toDF("text")
result = snomed_pipeline.transform(data)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val snomed_pipeline = PretrainedPipeline("sbiobertresolve_snomed_procedures_measurements_pipeline_20260901", "en", "clinical/models")
val data = Seq("The patient underwent a laparoscopic cholecystectomy and appendectomy. Laboratory testing showed an elevated white blood cell count.").toDF("text")
val result = snomed_pipeline.transform(data)
Results
| chunk | label | snomed_code | resolution | all_codes | all_resolutions |
|:-----------------------------|:----------|--------------:|:-----------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| laparoscopic cholecystectomy | Procedure | 45595009 | laparoscopic cholecystectomy | 45595009:::450500003:::440581009:::450499007:::67557008:::1137453008:::449334003:::38102005:::89967006:::1137372009:::174497004:::302619004:::1220546008:::1137362006:::1351803006:::6402000:::88748005:::708632008:::1162442001:::439712000:::6025007:::45993005 | laparoscopic cholecystectomy:::laparoscopic cholecystostomy:::laparoscopic cholecystenterostomy:::laparoscopic subtotal cholecystectomy:::laparoscopic cholecystectomy with exploration of common duct:::robot assisted laparoscopic cholecystectomy:::endoscopic choledocholithotomy:::cholecystectomy:::thoreck operation, partial cholecystectomy:::robot assisted laparoscopic partial cholecystectomy:::partial cholecystectomy and exploration of common bile duct:::cholecystectomy and exploration of bile duct:::laparoscopic jejunectomy:::robot assisted laparoscopic cholecystectomy and exploration of common bile duct:::laparoscopic cholecystectomy with intraoperative fluoroscopic cholangiography with contrast:::choledochectomy:::cholecystolithotomy:::laparoscopic incision and exploration of common bile duct:::laparoscopic hepatic cystectomy:::cholecystectomy with exploration of common bile duct and choledochoenterostomy:::laparoscopic appendicectomy:::cholecystectomy with exploration of common duct |
| appendectomy | Procedure | 80146002 | appendectomy | 80146002:::17041004:::82730006:::174045003:::6025007:::235314005:::51113007:::1299000:::49586007:::42332004:::49438003:::6801000:::39126001:::22324003:::54357003:::55588008:::174036004:::307583008:::119954001 | appendectomy:::appendicotomy:::secondary appendectomy:::interval appendectomy:::endoscopic appendectomy:::inversion appendectomy:::appendicolysis:::excision of appendiceal stump:::appendicocaecostomy:::appendicostomy:::appendectomy and drainage:::mesenterectomy:::angiectomy:::jejunectomy:::enterectomy:::abdominal arteriectomy:::emergency appendectomy:::cecectomy:::adenoidectomy |
| Laboratory testing | Test | 15220000 | laboratory test | 15220000:::386344002:::108252007:::16488004:::266753000:::410343006:::67664000:::18699002:::410394004:::117337005:::431561000124105:::56377008:::428995007:::57501001:::127789004:::252318005:::252511003:::33526004:::59615004 | laboratory test:::laboratory data interpretation:::laboratory procedures:::laboratory reporting:::referral for laboratory tests:::laboratory findings case management:::laboratory calculation:::clinical laboratory specimen identification:::laboratory findings surveillance:::calculated laboratory test method:::monitoring of laboratory results:::laboratory ratio determination:::receiving of specimen in laboratory:::laboratory reporting, cum sum:::laboratory procedure categorized by method:::immunology laboratory test:::clinical immunological test:::laboratory reporting, electronic:::laboratory test order by laboratory initiative |
| white blood cell count | Test | 767002 | white blood cell count | 767002:::252305002:::165511009:::44190001:::391558003:::42396003:::302560003:::250300004:::88308000:::6289009:::252306001:::19957009:::250305009:::118218001:::47616002:::250273000:::252276003 | white blood cell count:::white blood cell test:::differential white blood cell count:::white blood cell morphology:::total white blood cell count:::white blood cell estimate:::percentage differential white blood cells:::white blood cell enzyme activity:::blood cell count:::white blood cell histogram evaluation:::white blood cell cytochemistry:::white blood cell enzyme determination:::white blood cell membrane antigen:::cell count:::white blood cell localisation, whole body:::white blood cell age:::blood cell analysis |
Model Information
| Model Name: | sbiobertresolve_snomed_procedures_measurements_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