Description
This pretrained pipeline maps entities with their corresponding RxNorm codes. You’ll just feed your text and it will return the corresponding RxNorm codes.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("rxnorm_resolver_pipeline", "en", "clinical/models")
result = ner_pipeline.fullAnnotate("""The patient was prescribed Albuterol inhaler when needed. She was seen by the endocrinology service, prescribed Avandia 4 mg at nights,
Coumadin 5 mg with meals, Metformin 100 mg two times a day, and a daily dose of Lisinopril 10 mg.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("rxnorm_resolver_pipeline", "en", "clinical/models")
val result = ner_pipeline.fullAnnotate("""The patient was prescribed Albuterol inhaler when needed. She was seen by the endocrinology service, prescribed Avandia 4 mg at nights,
Coumadin 5 mg with meals, Metformin 100 mg two times a day, and a daily dose of Lisinopril 10 mg.""")
Results
+-----------------+-----+---+---------+-----------+---------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+
| chunk|begin|end|ner_label|rxnorm_code| resolved_text| all_codes| all_resolutions| all_k_aux_labels| all_distances|
+-----------------+-----+---+---------+-----------+---------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+
|Albuterol inhaler| 27| 43| DRUG| 745678| albuterol metered dose inhaler [albuterol metered dose inhaler]|745678:::2108226:::1154602:::2108233:::2108228:::1649559:::746762::...|albuterol metered dose inhaler [albuterol metered dose inhaler]:::a...|Clinical Drug Form:::Clinical Drug Form:::Clinical Dose Group:::Cli...|4.9847:::5.1028:::5.4746:::5.7809:::6.2859:::6.3948:::6.4499:::6.48...|
| Avandia 4 mg| 112|123| DRUG| 261242| rosiglitazone 4 MG Oral Tablet [Avandia]|261242:::810073:::153845:::1094008:::2123140:::1369735:::862026:::1...|rosiglitazone 4 MG Oral Tablet [Avandia]:::fesoterodine fumarate 4 ...|Branded Drug:::Branded Drug Comp:::Branded Drug:::Branded Drug Comp...|0.0000:::4.7482:::5.0125:::5.2516:::5.4650:::5.4880:::5.4964:::5.56...|
| Coumadin 5 mg| 136|148| DRUG| 855333| warfarin sodium 5 MG [Coumadin]|855333:::438740:::153692:::352120:::1036890:::104363:::201269:::351...|warfarin sodium 5 MG [Coumadin]:::coumarin 5 mg [coumarin 5 mg]:::o...|Branded Drug Comp:::Clinical Drug Comp:::Branded Drug:::Branded Dru...|0.0000:::4.0885:::5.3065:::5.5132:::5.5336:::5.7412:::5.8485:::6.03...|
| Metformin 100 mg| 162|177| DRUG| 861024|metformin hydrochloride 100 mg/ml [metformin hydrochloride 100 mg/ml]|861024:::334738:::332848:::861026:::333262:::429178:::103910:::4294...|metformin hydrochloride 100 mg/ml [metformin hydrochloride 100 mg/m...|Clinical Drug Comp:::Clinical Drug Comp:::Clinical Drug Comp:::Bran...|6.3835:::6.5293:::6.5728:::6.9061:::6.9297:::6.9512:::6.9935:::7.09...|
| Lisinopril 10 mg| 216|231| DRUG| 314076| lisinopril 10 MG Oral Tablet|314076:::567576:::565846:::389184:::563611:::328290:::857169:::3127...|lisinopril 10 MG Oral Tablet:::lisinopril 10 mg [prinivil] [lisinop...|Clinical Drug:::Branded Drug Comp:::Branded Drug Comp:::Clinical Dr...|0.0000:::3.6543:::4.2783:::4.2805:::4.6016:::5.1265:::5.5412:::5.72...|
+-----------------+-----+---+---------+-----------+---------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+
Model Information
| Model Name: | rxnorm_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.4.0+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 3.3 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- TextMatcherInternalModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel