Description
This pretrained pipeline extracts medication entities and maps them to their corresponding RxNorm codes.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("rxnorm_resolver_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""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.annotate("""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 5.3.3+ |
| 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