Description
This advanced pipeline extracts drug entities from clinical texts and utilizes the sbiobert_base_cased_mli Sentence Bert Embeddings to map these entities to their corresponding SNOMED codes.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("snomed_drug_resolver_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""John's doctor prescribed aspirin for his heart condition,
along with paracetamol for his fever and headache, amoxicillin for his tonsilitis and
lansoprazole for his GORD on 2023-12-01.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("snomed_drug_resolver_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""John's doctor prescribed aspirin for his heart condition,
along with paracetamol for his fever and headache, amoxicillin for his tonsilitis and
lansoprazole for his GORD on 2023-12-01.""")
Results
+------------+-----+---+---------+---------+------------+------------------------------------------------------------+------------------------------------------------------------+
| chunk|begin|end|ner_label| code| description| all_codes| resolutions|
+------------+-----+---+---------+---------+------------+------------------------------------------------------------+------------------------------------------------------------+
| aspirin| 25| 31| DRUG| 7947003| aspirin|7947003:::358427004:::426365001:::412566001:::25796002:::...|aspirin:::oral aspirin:::aspirin, buffered:::buffered asp...|
| paracetamol| 69| 79| DRUG|387517004| paracetamol|387517004:::90332006:::437876006:::437818001:::322998004:...|paracetamol:::paracetamol product:::oral form paracetamol...|
| amoxicillin| 109|119| DRUG| 27658006| amoxicillin|27658006:::350162003:::427483001:::350164002:::117147001:...|amoxicillin:::oral amoxicillin:::amoxicillin sodium:::ora...|
|lansoprazole| 144|155| DRUG|108666007|lansoprazole|108666007:::437961004:::441863009:::716069007:::108840006...|lansoprazole:::oral form lansoprazole:::dexlansoprazole::...|
+------------+-----+---+---------+---------+------------+------------------------------------------------------------+------------------------------------------------------------+
Model Information
| Model Name: | snomed_drug_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.3.0+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.4 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- TextMatcherInternalModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel