Description
This pipeline extracts clinical entities from text and maps them to the full, domain-unrestricted set of active SNOMED CT concepts using sbiobert_base_cased_mli_onnx embeddings.
Wraps the sbiobertresolve_snomed_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_pipeline_20260901", "en", "clinical/models")
data = spark.createDataFrame([["The patient with inflammatory bowel disease presented with dyspnea and abdominal pain. She underwent a laparoscopic appendectomy and was started on aspirin."]]).toDF("text")
result = snomed_pipeline.transform(data)
from johnsnowlabs import nlp, medical
snomed_pipeline = nlp.PretrainedPipeline("sbiobertresolve_snomed_pipeline_20260901", "en", "clinical/models")
data = spark.createDataFrame([["The patient with inflammatory bowel disease presented with dyspnea and abdominal pain. She underwent a laparoscopic appendectomy and was started on aspirin."]]).toDF("text")
result = snomed_pipeline.transform(data)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val snomed_pipeline = PretrainedPipeline("sbiobertresolve_snomed_pipeline_20260901", "en", "clinical/models")
val data = Seq("The patient with inflammatory bowel disease presented with dyspnea and abdominal pain. She underwent a laparoscopic appendectomy and was started on aspirin.").toDF("text")
val result = snomed_pipeline.transform(data)
Results
| chunk | label | snomed_code | resolution | all_codes | all_resolutions |
|:---------------------------|:--------------------------|--------------:|:---------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| inflammatory bowel disease | Disease_Syndrome_Disorder | 24526004 | inflammatory bowel disease | 24526004:::9281000146109:::6382002:::1300120005:::1300124001:::700104004:::128999004:::373407002:::1162893000:::788718000:::10743008:::82196007:::608844008:::397173003:::397172008:::403878007:::128139000:::737195007:::50440006:::1144956000:::1187638005:::274897005 | inflammatory bowel disease:::inflammatory bowel disease suspected:::chronic inflammatory small bowel disease:::alpi-related inflammatory bowel disease:::trim22-related inflammatory bowel disease:::management of inflammatory bowel disease:::inflammatory disorder of digestive tract:::inflammatory disorder of digestive system:::bowen's disease:::iritis co-occurrent with inflammatory bowel disease:::functional bowel disease:::ischaemic bowel disease:::history of inflammatory bowel disease:::crohn's disease of intestine:::gastrointestinal crohn's disease:::bowen's disease of arm:::inflammatory disease:::crohn disease of upper gastrointestinal tract:::granulomatous colitis:::vasculitis due to inflammatory bowel disease:::inflammation of intestine:::clonal bowen's disease |
| dyspnea | Symptom | 267036007 | dyspnea | 267036007:::60845006:::25209001:::34560001:::59265000:::870535009:::1023001:::386614005:::90701007:::161939006:::390871002:::30744009:::62744007 | dyspnea:::exertional dyspnea:::inspiratory dyspnea:::expiratory dyspnea:::paroxysmal dyspnea:::chronic dyspnea:::apnea:::oligopnea:::secondary apnea:::dyspnea on moderate exertion:::dyspnea on strenuous exertion:::platypnea:::orthopnea |
| abdominal pain | Symptom | 21522001 | abdominal pain | 21522001:::83132003:::364630006:::162042000:::247358007:::438506002:::102614006:::102613000:::14700001000004102:::9991008:::162046002:::1332010007:::28221000119103:::35611005:::111985007:::307199009:::73645008:::737306007:::29695002:::275406005 | abdominal pain:::upper abdominal pain:::abdominal pain characteristic:::abdominal wall pain:::abdominal pain type:::visceral abdominal pain:::generalized abdominal pain:::localized abdominal pain:::intractable abdominal pain:::colicky abdominal pain:::central abdominal pain:::site of abdominal pain:::abdominal muscle pain:::abdominal rebound pain:::chronic abdominal pain:::psychosomatic abdominal pain:::visceral pain:::chronic visceral pain:::throbbing pain:::appendicular pain |
| laparoscopic appendectomy | Procedure | 6025007 | laparoscopic appendectomy | 6025007:::307581005:::708819001:::1220546008:::174041007:::46569000:::235314005:::708876004:::1390003:::708627007:::80146002:::1220549001:::45595009:::42843004:::1255832001 | laparoscopic appendectomy:::laparoscopic interval appendectomy:::laparoscopic omentectomy:::laparoscopic jejunectomy:::laparoscopic emergency appendectomy:::laparoscopic-assisted abdominoperineal resection:::inversion appendectomy:::robot assisted laparoscopic appendectomy:::laparoscopic-assisted sigmoidectomy:::laparoscopic excision of small intestine:::appendectomy:::laparoscopic ileectomy:::laparoscopic cholecystectomy:::laparoscopic adrenalectomy:::laparoscopic anorectoplasty |
| aspirin | Drug_Ingredient | 387458008 | aspirin | 387458008:::432909005:::135800003:::717854002:::7947003:::431463004:::405742008:::417980006:::426365001:::405743003:::407136004:::412566001:::25796002:::312452009:::26047008:::405748007:::87303007:::319796006:::398767009:::390882005:::785413006 | aspirin:::aspirin given:::aspirin indicated:::aspirin therapy:::aspirin-containing product:::administration of aspirin:::aspirin therapy finding:::contains aspirin:::aspirin, buffered:::aspirin therapy location:::aspirin specific ige:::buffered aspirin-containing product:::aluminium aspirin:::aspirin prophylaxis:::aspirin tolerance test:::already on aspirin:::cephapirin:::aspirin- and dipyridamole-containing product:::aspirin- and glycine-containing product:::referral to gp - aspirin management:::aspirin-containing product in oromucosal dose form |
Model Information
| Model Name: | sbiobertresolve_snomed_pipeline_20260901 |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 6.4.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 4.2 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel