Description
This pipeline extracts clinical entities from text and maps them to SNOMED CT concepts not assigned to a specific class using sbiobert_base_cased_mli_onnx embeddings.
Wraps the sbiobertresolve_snomed_no_class_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_no_class_pipeline_20260901", "en", "clinical/models")
data = spark.createDataFrame([["The patient developed postsurgical gastroparesis after her procedure. Pathology confirmed a malignant gastroblastoma. On eye exam she was also noted to have trichiasis of upper eyelid."]]).toDF("text")
result = snomed_pipeline.transform(data)
from johnsnowlabs import nlp, medical
snomed_pipeline = nlp.PretrainedPipeline("sbiobertresolve_snomed_no_class_pipeline_20260901", "en", "clinical/models")
data = spark.createDataFrame([["The patient developed postsurgical gastroparesis after her procedure. Pathology confirmed a malignant gastroblastoma. On eye exam she was also noted to have trichiasis of upper eyelid."]]).toDF("text")
result = snomed_pipeline.transform(data)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val snomed_pipeline = PretrainedPipeline("sbiobertresolve_snomed_no_class_pipeline_20260901", "en", "clinical/models")
val data = Seq("The patient developed postsurgical gastroparesis after her procedure. Pathology confirmed a malignant gastroblastoma. On eye exam she was also noted to have trichiasis of upper eyelid.").toDF("text")
val result = snomed_pipeline.transform(data)
Results
| chunk | label | snomed_code | resolution | all_codes | all_resolutions |
|:---------------------------|:--------------------------|----------------:|:-----------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| gastroparesis | Disease_Syndrome_Disorder | 1397402007 | postsurgical gastroparesis | 1397402007:::440295211000119108:::1396770008:::1389031007:::1389007002:::1384135004:::1388584008:::510204201000119100:::1399444005:::1389191007:::1396814004:::1396027004:::1395863006:::465961000087104 | postsurgical gastroparesis:::intestinal failure:::type 2 intestinal failure:::esophageal spasm:::ifald - intestinal failure associated liver disease:::assessment of nutritional disorder:::gastric dilatation:::autoimmune gastritis:::gastric burping:::distal esophageal spasm:::recurrent giardia lamblia intestinal infection:::erosion of mucous membrane of large intestine:::bleeding superficial ulcer of stomach:::right thoracic radiculopathy |
| malignant gastroblastoma | Oncological | 2711000181102 | malignant gastroblastoma | 2711000181102:::1395929008:::112751000112108:::1388817002:::1388815005:::1388810000:::1388811001:::1388814009:::1388813003 | malignant gastroblastoma:::mixed glioma of brain:::gist (gastrointestinal stromal tumor) suspected:::malignant succinate dehydrogenase-deficient renal cell carcinoma:::malignant fumarate hydratase-deficient renal cell carcinoma:::malignant eloc-mutated renal cell carcinoma:::malignant alk-rearranged renal cell carcinoma:::malignant tfeb-altered renal cell carcinoma:::malignant tfe3-rearranged renal cell carcinoma |
| trichiasis of upper eyelid | Disease_Syndrome_Disorder | 412041000087109 | entropion and trichiasis of upper eyelid | 412041000087109:::412031000087103:::412021000087100:::412001000087106:::331531000119106:::1389166007:::11854611000119104:::1395935008:::412011000087108:::15998671000119101:::699881010000107:::1397845007:::408631000087107:::1397358000:::1397511009:::1388547006:::1388359009:::1396995000:::1396238009:::11854571000119108 | entropion and trichiasis of upper eyelid:::entropion and trichiasis of right upper eyelid:::entropion and trichiasis of right lower eyelid:::entropion and trichiasis of left upper eyelid:::spastic ectropion of right upper eyelid:::infected blister of eyelid:::infected blister of right eyelid:::wet line of upper lip:::entropion and trichiasis of lower eyelid:::cysticercosis of right eye:::lens esculenta igg:::subretinal hyperreflective material on optical coherence tomography:::contact dermatitis of skin of upper arm:::intraretinal cystoid space on optical coherence tomography:::excoriation disorder:::granulomatous uveitis:::ultrasonography of eye region abnormal:::ifag - idiopathic facial aseptic granuloma:::acne tarda:::traumatic blister of right eyelid |
Model Information
| Model Name: | sbiobertresolve_snomed_no_class_pipeline_20260901 |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 6.4.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.2 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel