Description
This advanced pipeline extracts medical entities from clinical texts and utilizes the sbiobert_base_cased_mli Sentence Bert Embeddings to map these entities to their corresponding RxNorm Concept Unique Identifier (RxCUI) codes.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("rxcui_resolver_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""He was seen by the endocrinology service and she was discharged on 50 mg of eltrombopag oral at night, 5 mg amlodipine with meals, and metformin 1000 mg two times a day.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("rxcui_resolver_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""He was seen by the endocrinology service and she was discharged on 50 mg of eltrombopag oral at night, 5 mg amlodipine with meals, and metformin 1000 mg two times a day.""")
Results
+-------------------------+-----+---+---------+------+-------------------------------------------+------------------------------------------------------------+------------------------------------------------------------+
| chunk|begin|end|ner_label| Code| description| resolutions| all_codes|
+-------------------------+-----+---+---------+------+-------------------------------------------+------------------------------------------------------------+------------------------------------------------------------+
|50 mg of eltrombopag oral| 67| 91| DRUG|825427| eltrombopag 50 MG Oral Tablet|eltrombopag 50 MG Oral Tablet:::alpelisib 50 MG Oral Tabl...|825427:::2169316:::2049111:::1804806:::1940374:::1597587:...|
| 5 mg amlodipine| 103|117| DRUG|197361| amlodipine 5 MG Oral Tablet|amlodipine 5 MG Oral Tablet:::levamlodipine 5 MG Oral Tab...|197361:::2377371:::387013:::212549:::311354:::2377373:::4...|
| metformin 1000 mg| 135|151| DRUG|861004|metformin hydrochloride 1000 MG Oral Tablet|metformin hydrochloride 1000 MG Oral Tablet:::cefepime 10...|861004:::1665093:::1791593:::311625:::1665050:::1722919::...|
+-------------------------+-----+---+---------+------+-------------------------------------------+------------------------------------------------------------+------------------------------------------------------------+
Model Information
| Model Name: | rxcui_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.2.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.2 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel