Clinical Ner Assertion

Description

A pretrained pipeline with ner_clinical and assertion_dl. It will extract clinical entities and assign assertion status for them.

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How to use

pipeline = PretrainedPipeline("clinical_ner_assertion","en","clinical/models")

result = pipe_model.fullAnnotate("""She is admitted to The John Hopkins Hospital 2 days ago with a history of gestational diabetes mellitus diagnosed. She denied pain and any headache.She was seen by the endocrinology service and she was discharged on 03/02/2018 on 40 units of insulin glargine, 12 units of insulin lispro, and metformin 1000 mg two times a day. She had close follow-up with endocrinology post discharge.""")[0]

result.keys()
val pipeline = new PretrainedPipeline("clinical_ner_assertion","en","clinical/models")

val result = pipeline.fullAnnotate("She is admitted to The John Hopkins Hospital 2 days ago with a history of gestational diabetes mellitus diagnosed. She denied pain and any headache.She was seen by the endocrinology service and she was discharged on 03/02/2018 on 40 units of insulin glargine, 12 units of insulin lispro, and metformin 1000 mg two times a day. She had close follow-up with endocrinology post discharge.")(0)

Results


                          chunks  entities  assertion

0  gestational diabetes mellitus   PROBLEM  present
1                           pain   PROBLEM  absent
2                       headache   PROBLEM  absent
3               insulin glargine TREATMENT  present
4                 insulin lispro TREATMENT  present
5                      metformin TREATMENT  present

Model Information

Name: clinical_ner_assertion
Type: PipelineModel
Compatibility: Spark NLP 2.4.0+
License: Licensed
Edition: Official
Language: en

Included Models

  • ner_clinical
  • assertion_dl