Description
This pipeline extracts clinical entities from text and maps them to the full, domain-unrestricted set of active SNOMED CT concepts using mpnet_embeddings_biolord_2023_c embeddings.
Wraps the biolordresolve_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("biolordresolve_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("biolordresolve_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("biolordresolve_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:::1396343004:::64226004:::1187638005:::43752006:::50440006:::397173003:::34000006:::52457000:::64766004:::396336000:::54597004:::418130002 | inflammatory bowel disease:::inflammatory bowel disease unclassified:::colitis:::enteritis of intestine:::inflammation of small intestine and colon:::cc - crohn's colitis:::crohn disease of intestine:::crohn disease:::ileitis:::colitis gravis:::acute and chronic colitis:::chronic colitis:::colorectitis |
| dyspnea | Symptom | 267036007 | dyspnea | 267036007:::297216006:::230145002:::248549001:::23141003:::60845006:::870535009:::399322006:::248550001 | dyspnea:::increasing breathlessness:::difficulty breathing:::labored breathing:::gasping for breath:::soboe - shortness of breath on exertion:::chronic dyspnea:::air hunger:::can't breathe deeply enough |
| abdominal pain | Symptom | 21522001 | abdominal pain | 21522001:::9991008:::271681002:::102614006:::73063007:::438506002:::162042000:::247358007:::162046002:::54586004:::116290004:::371102005:::102613000:::443503005:::304542004:::410716004 | abdominal pain:::abdominal colic:::belly ache:::generalised abdominal pain:::colicky pain:::visceral abdominal pain:::abdominal wall pain:::abdominal pain type:::central abdominal pain:::lower abdominal pain:::acute abdominal pain:::generalised colicky abdominal pain:::localised abdominal pain:::periumbilical abdominal pain:::nonspecific abdominal pain:::colicky |
| laparoscopic appendectomy | Procedure | 6025007 | laparoscopic appendectomy | 6025007:::307581005:::708876004:::174041007:::80146002:::440588003:::235313004:::82730006:::1156321000:::174045003:::174036004 | laparoscopic appendectomy:::laparoscopic interval appendectomy:::robot assisted laparoscopic appendectomy:::laparoscopic emergency appendectomy:::appendectomy:::endoscopic procedure on appendix:::non-emergency appendectomy:::incidental appendectomy:::history of laparoscopic appendectomy:::interval appendicectomy:::emergency appendicectomy |
| aspirin | Drug_Ingredient | 387458008 | aspirin | 387458008:::7947003:::426365001:::25796002:::10876551000119102:::60526005:::292044008:::412566001:::417980006:::295135004:::717854002:::255637000:::431463004:::418281004:::774656009:::405748007:::293586001:::8132009:::135800003:::350312004 | aspirin:::aspirin-containing product:::buffered aspirin:::aluminum aspirin:::aspirin poisoning:::acetyl salicylate:::aspirin adverse reaction:::buffered aspirin-containing product:::contains aspirin:::aspirin overdose:::aspirin therapy:::salicylate:::administration of aspirin:::do not take anything containing aspirin while taking this medicine:::aspirin only product:::already on aspirin:::aspirin allergy:::magnesium acetylsalicylate:::aspirin indicated:::product containing salicylate |
Model Information
| Model Name: | biolordresolve_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
- MPNetEmbeddings
- SentenceEntityResolverModel