Explain Clinical Document Pipeline - CARP

Description

A pipeline with ner_clinical, assertion_dl, re_clinical and ner_posology. It will extract clinical and medication entities, assign assertion status and find relationships between clinical entities.

Live Demo Open in Colab Download

How to use

carp_pipeline = PretrainedPipeline("explain_clinical_doc_carp","en","clinical/models")

annotations =  carp_pipeline.fullAnnotate("""A 28-year-old female with a history of gestational diabetes mellitus, used to take metformin 1000 mg two times a day, presented with a one-week history of polyuria , polydipsia , poor appetite , and vomiting. She was seen by the endocrinology service and discharged on 40 units of insulin glargine at night, 12 units of insulin lispro with meals.""")[0]

annotations.keys()
val carp_pipeline = new PretrainedPipeline("explain_clinical_doc_carp","en","clinical/models")

val result = carp_pipeline.fullAnnotate("""A 28-year-old female with a history of gestational diabetes mellitus, used to take metformin 1000 mg two times a day, presented with a one-week history of polyuria , polydipsia , poor appetite , and vomiting. She was seen by the endocrinology service and discharged on 40 units of insulin glargine at night, 12 units of insulin lispro with meals.""")(0)

Results

|   | chunks                        | ner_clinical | assertion | posology_chunk   | ner_posology | relations |
|---|-------------------------------|--------------|-----------|------------------|--------------|-----------|
| 0 | gestational diabetes mellitus | PROBLEM      | present   | metformin        | Drug         | TrAP      |
| 1 | metformin                     | TREATMENT    | present   | 1000 mg          | Strength     | TrCP      |
| 2 | polyuria                      | PROBLEM      | present   | two times a day  | Frequency    | TrCP      |
| 3 | polydipsia                    | PROBLEM      | present   | 40 units         | Dosage       | TrWP      |
| 4 | poor appetite                 | PROBLEM      | present   | insulin glargine | Drug         | TrCP      |
| 5 | vomiting                      | PROBLEM      | present   | at night         | Frequency    | TrAP      |
| 6 | insulin glargine              | TREATMENT    | present   | 12 units         | Dosage       | TrAP      |

Model Information

Model Name: explain_clinical_doc_carp
Type: pipeline
Compatibility: Spark NLP for Healthcare 3.0.0+
License: Licensed
Edition: Official
Language: en