Pipeline to Detect Adverse Drug Events (langtest)

Description

This pretrained pipeline is built on the top of ner_ade_clinical_langtest model.

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How to use


from sparknlp.pretrained import PretrainedPipeline

ner_pipeline = PretrainedPipeline("ner_ade_clinical_langtest_pipeline", "en", "clinical/models")

result = ner_pipeline.annotate("""I asked my doctor what could have caused this, and he said it was probably from the Lipitor. Recently I experienced extreme stomach pain that stretched to my side and back. The stomach pain came suddenly and it would come and go for a week before it became so bad I could not sleep. I had just gotten over a urinary tract infection (one of the side-effects) and I thought it had returned, but the symptoms were different. I still had the urge to urinate constantly, but it would come and go, and I would have no symptoms for a day, then it would return again. I remembered reading the pamphlet that comes with the prescription drugs, and it mentioning some of the symptoms that I was experiencing. I stopped taking the Lipitor for a day, and I did not have any more stomach pain or urgency. I also had been experiencing lack of energy for quite some time, and I attributed this to stress, but after reading this website, I feel it was due to the Lipitor also. I don't think I will take this drug anymore, and since I read that taking vitamin C can help you with your cholesterol, I think I will try this method instead. I think there should be a better alternative to lowering cholesterol than such a potent drug that can cause so many side effects. I don't want to be a case-study when they finally take this drug off the market.""")


import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline

val ner_pipeline = PretrainedPipeline("ner_ade_clinical_langtest_pipeline", "en", "clinical/models")

val result = ner_pipeline.annotate("""I asked my doctor what could have caused this, and he said it was probably from the Lipitor. Recently I experienced extreme stomach pain that stretched to my side and back. The stomach pain came suddenly and it would come and go for a week before it became so bad I could not sleep. I had just gotten over a urinary tract infection (one of the side-effects) and I thought it had returned, but the symptoms were different. I still had the urge to urinate constantly, but it would come and go, and I would have no symptoms for a day, then it would return again. I remembered reading the pamphlet that comes with the prescription drugs, and it mentioning some of the symptoms that I was experiencing. I stopped taking the Lipitor for a day, and I did not have any more stomach pain or urgency. I also had been experiencing lack of energy for quite some time, and I attributed this to stress, but after reading this website, I feel it was due to the Lipitor also. I don't think I will take this drug anymore, and since I read that taking vitamin C can help you with your cholesterol, I think I will try this method instead. I think there should be a better alternative to lowering cholesterol than such a potent drug that can cause so many side effects. I don't want to be a case-study when they finally take this drug off the market.""")

Results

|    | chunks                     |   begin |   end | entities   |
|---:|:---------------------------|--------:|------:|:-----------|
|  0 | the Lipitor                |      80 |    90 | DRUG       |
|  1 | stomach pain               |     124 |   135 | ADE        |
|  2 | back                       |     167 |   170 | ADE        |
|  3 | stomach pain               |     177 |   188 | ADE        |
|  4 | urinary tract infection    |     308 |   330 | ADE        |
|  5 | urge to urinate constantly |     438 |   463 | ADE        |
|  6 | the prescription drugs     |     610 |   631 | DRUG       |
|  7 | the Lipitor                |     715 |   725 | DRUG       |
|  8 | lack of energy             |     820 |   833 | ADE        |
|  9 | Lipitor                    |     946 |   952 | DRUG       |
| 10 | vitamin C                  |    1034 |  1042 | DRUG       |
| 11 | I don't                    |    1250 |  1256 | DRUG       |

Model Information

Model Name: ner_ade_clinical_langtest_pipeline
Type: pipeline
Compatibility: Healthcare NLP 5.1.0+
License: Licensed
Edition: Official
Language: en
Size: 1.7 GB

Included Models

  • DocumentAssembler
  • SentenceDetectorDLModel
  • TokenizerModel
  • WordEmbeddingsModel
  • MedicalNerModel
  • NerConverterInternalModel