Description
A pretrained pipeline with ner_clinical, assertion_dl, re_clinical. It will extract clinical entities, assign assertion status and find relationships between clinical entities.
How to use
cra_pipeline = PretrainedPipeline("explain_clinical_doc_cra","en","clinical/models")
annotations = cra_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]
annotations.keys()
val cra_pipeline = new PretrainedPipeline("explain_clinical_doc_cra","en","clinical/models")
val result = cra_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
This pretrained pipeline gives the result of ner_clinical, re_clinical and assertion_dl models.
| | chunk1 | ner_clinical1 | assertion | relation | chunk2 | ner_clinical2 |
|---|-------------------------------|---------------|------------|----------|---------------|---------------|
| 0 | gestational diabetes mellitus | PROBLEM | present | TrAP | metformin | TREATMENT |
| 1 | gestational diabetes mellitus | PROBLEM | present | TrAP | polyuria | PROBLEM |
| 2 | gestational diabetes mellitus | PROBLEM | present | TrCP | polydipsia | PROBLEM |
| 3 | gestational diabetes mellitus | PROBLEM | present | TrCP | poor appetite | PROBLEM |
| 4 | metformin | TREATMENT | present | TrAP | polyuria | PROBLEM |
| 5 | metformin | TREATMENT | present | TrAP | polydipsia | PROBLEM |
| 6 | metformin | TREATMENT | present | TrAP | poor appetite | PROBLEM |
| 7 | polydipsia | PROBLEM | present | TrAP | vomiting | PROBLEM |
Model Information
| Name: | explain_clinical_doc_cra |
| Type: | PipelineModel |
| Compatibility: | Spark NLP 2.5.5+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
Included Models
- ner_clinical
- assertion_dl
- re_clinical