Description
This pipeline extracts clinical entities from text and maps them to SNOMED CT body structure concepts using sbiobert_base_cased_mli_onnx embeddings.
Wraps the sbiobertresolve_snomed_bodyStructure_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_bodyStructure_pipeline_20260901", "en", "clinical/models")
data = spark.createDataFrame([["The patient is a 30-year-old female with coronary artery disease and swelling affecting the kidney and lower limb."]]).toDF("text")
result = snomed_pipeline.transform(data)
from johnsnowlabs import nlp, medical
snomed_pipeline = nlp.PretrainedPipeline("sbiobertresolve_snomed_bodyStructure_pipeline_20260901", "en", "clinical/models")
data = spark.createDataFrame([["The patient is a 30-year-old female with coronary artery disease and swelling affecting the kidney and lower limb."]]).toDF("text")
result = snomed_pipeline.transform(data)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val snomed_pipeline = PretrainedPipeline("sbiobertresolve_snomed_bodyStructure_pipeline_20260901", "en", "clinical/models")
val data = Seq("The patient is a 30-year-old female with coronary artery disease and swelling affecting the kidney and lower limb.").toDF("text")
val result = snomed_pipeline.transform(data)
Results
| chunk | label | snomed_code | resolution | all_codes | all_resolutions |
|:----------------|:---------|--------------:|:----------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| coronary artery | BodyPart | 41801008 | coronary artery | 41801008:::119204004:::360487004:::55537005:::110554000:::48955001:::1343313006:::57627008:::280515006:::713317004:::110755001:::57396003:::360511005:::1373794005:::244252004:::110553006:::69105007 | coronary artery:::coronary artery part:::segment of coronary artery:::ostium of coronary artery:::coronary artery and coronary artery, cs:::coronary valve:::structure of lumen of coronary artery:::coronary ligament:::coronary plexus:::structure of wall of coronary artery:::aorta and coronary artery, cs:::structure of circumflex coronary artery:::segment of circumflex coronary artery:::ostium of coronary intermediate artery:::structure of coronary intermediate artery:::coronary artery and myocardium, cs:::carotid artery structure |
| kidney | BodyPart | 64033007 | kidney | 64033007:::119219003:::84924000:::50403003:::72333003:::30737000:::74033008:::58471003:::303402001:::363530009:::363529004:::54018001:::29704000:::279371005:::16097006:::27788008:::116358006:::363531008:::91678002 | kidney:::kidney part:::renal segment:::renal cortex:::capillary of kidney:::medulla of kidney:::hilum of kidney:::renal tubule:::renal vessels:::structure of region of kidney:::structure of layer of kidney:::nephron:::parenchyma of kidney:::renal collecting system structure:::renal pyramid:::renal tubular neck:::vein of kidney:::structure of pole of kidney:::lateral border of kidney |
| lower limb | BodyPart | 61685007 | lower limb | 61685007:::30021000:::63337009:::128263001:::120575009:::69548008:::48077000:::37822005:::32032005:::27033000:::82094008:::127951001:::281394001:::39278005:::62736007:::264079000 | lower limb:::lower leg:::lower trunk:::lower body:::lower limb part:::lower body part:::lower jaw:::lower back structure:::lower lip:::lower abdomen structure:::lower respiratory structure:::lower extremity region:::lower zone of lung:::lower respiratory spaces:::lower eyelid:::lower pole artery |
Model Information
| Model Name: | sbiobertresolve_snomed_bodyStructure_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
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel