Explain Clinical Document - Granular

Description

This pipeline is designed to:

extract clinical entities
assign assertion status to the extracted entities
establish relations between the extracted entities

from clinical texts. In this pipeline, ner_jsl NER model, assertion_jsl assertion model, re_test_result_date, and posology_re relation extraction models were used to achieve those tasks. Here are the NER, assertion, and relation extraction labels this pipeline can extract. Here are the NER, assertion, and relation extraction labels this pipeline can extract.

Clinical Entity Labels: Admission_Discharge Age Alcohol Allergen BMI Birth_Entity Blood_Pressure Cerebrovascular_Disease Clinical_Dept Communicable_Disease Date Death_Entity Diabetes Diet Direction Disease_Syndrome_Disorder Dosage Drug_BrandName Drug_Ingredient Duration EKG_Findings Employment External_body_part_or_region Family_History_Header Fetus_NewBorn Form Frequency Gender HDL Heart_Disease Height Hyperlipidemia Hypertension ImagingFindings Imaging_Technique Injury_or_Poisoning Internal_organ_or_component Kidney_Disease LDL Labour_Delivery Medical_Device Medical_History_Header Modifier O2_Saturation Obesity Oncological Overweight Oxygen_Therapy Pregnancy Procedure Psychological_Condition Pulse Race_Ethnicity Relationship_Status RelativeDate RelativeTime Respiration Route Section_Header Sexually_Active_or_Sexual_Orientation Smoking Social_History_Header Strength Substance Substance_Quantity Symptom Temperature Test Test_Result Time Total_Cholesterol Treatment Triglycerides VS_Finding Vaccine Vaccine_Name Vital_Signs_Header Weight
Assertion Status Labels: Hypothetical, Someoneelse, Past, Absent, Family, Planned, Possible, Present
Relation Extraction Labels: is_finding_of, is_date_of, is_result_of, Drug_BrandName-Dosage, Drug_BrandName-Frequency, Drug_BrandName-Route , Drug_BrandName-Strength, Drug_Ingredient-Dosage, Drug_Ingredient-Frequency, Drug_Ingredient-Route, Drug_Ingredient-Strength, O

Download Copy S3 URI

How to use

from sparknlp.pretrained import PretrainedPipeline

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

result = ner_pipeline.annotate("""The patient admitted for gastrointestinal pathology, under working treatment.
History of prior heart murmur with echocardiogram findings as above on March 1998.
According to the latest echocardiogram, basically revealed normal left ventricular function with left atrial enlargement .
Based on the above findings, we will treat her medically with ACE inhibitors 10 mg, p.o, daily. Also we will give Furosemide 40 mg, p.o later and see how she fares.""")

import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline

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

val result = ner_pipeline.annotate("""The patient admitted for gastrointestinal pathology, under working treatment.
History of prior heart murmur with echocardiogram findings as above on March 1998.
According to the latest echocardiogram, basically revealed normal left ventricular function with left atrial enlargement .
Based on the above findings, we will treat her medically with ACE inhibitors 10 mg, p.o, daily. Also we will give Furosemide 40 mg, p.o later and see how she fares.""")

Results

# ner

+-----------+-----+---+--------------------------+-------------------+
|sentence_id|begin|end|entity                    |label              |
+-----------+-----+---+--------------------------+-------------------+
|0          |12   |19 |admitted                  |Admission_Discharge|
|0          |25   |50 |gastrointestinal pathology|Clinical_Dept      |
|1          |95   |106|heart murmur              |Heart_Disease      |
|1          |113  |126|echocardiogram            |Test               |
|1          |149  |158|March 1998                |Date               |
|2          |185  |198|echocardiogram            |Test               |
|2          |220  |225|normal                    |Test_Result        |
|2          |227  |251|left ventricular function |Test               |
|2          |258  |280|left atrial enlargement   |Heart_Disease      |
|3          |327  |329|her                       |Gender             |
|3          |346  |359|ACE inhibitors            |Drug_Ingredient    |
|3          |361  |365|10 mg                     |Strength           |
|3          |368  |370|p.o                       |Route              |
|3          |373  |377|daily                     |Frequency          |
|4          |398  |407|Furosemide                |Drug_Ingredient    |
|4          |409  |413|40 mg                     |Strength           |
|4          |416  |418|p.o                       |Route              |
|4          |438  |440|she                       |Gender             |
+-----------+-----+---+--------------------------+-------------------+

# assertion

+-----------+-----+---+-------------------------+---------------+----------------+
|sentence_id|begin|end|entity                   |label          |assertion_status|
+-----------+-----+---+-------------------------+---------------+----------------+
|1          |95   |106|heart murmur             |Heart_Disease  |Past            |
|1          |113  |126|echocardiogram           |Test           |Past            |
|2          |185  |198|echocardiogram           |Test           |Present         |
|2          |220  |225|normal                   |Test_Result    |Present         |
|2          |227  |251|left ventricular function|Test           |Present         |
|2          |258  |280|left atrial enlargement  |Heart_Disease  |Present         |
|3          |346  |359|ACE inhibitors           |Drug_Ingredient|Planned         |
|4          |398  |407|Furosemide               |Drug_Ingredient|Planned         |
+-----------+-----+---+-------------------------+---------------+----------------+

# relation

+-----------+-------------------------+---------------------+-------------------------+---------------------+-------------------------+--------------------------+----------------------------------+---------------------------------+----------------------------------+---------------------------------+-------------------------+--------------------------+-------------------------+--------------------------+-------------------------+
|sentence_id|all_relations            |all_relations_entity1|all_relations_chunk1     |all_relations_entity2|all_relations_chunk2     |test_result_date_relations|test_result_date_relations_entity1|test_result_date_relations_chunk1|test_result_date_relations_entity2|test_result_date_relations_chunk2|posology_relations       |posology_relations_entity1|posology_relations_chunk1|posology_relations_entity2|posology_relations_chunk2|
+-----------+-------------------------+---------------------+-------------------------+---------------------+-------------------------+--------------------------+----------------------------------+---------------------------------+----------------------------------+---------------------------------+-------------------------+--------------------------+-------------------------+--------------------------+-------------------------+
|1          |is_finding_of            |Heart_Disease        |heart murmur             |Test                 |echocardiogram           |is_finding_of             |Heart_Disease                     |heart murmur                     |Test                              |echocardiogram                   |Drug_Ingredient-Strength |Drug_Ingredient           |ACE inhibitors           |Strength                  |10 mg                    |
|1          |is_date_of               |Heart_Disease        |heart murmur             |Date                 |March 1998               |is_date_of                |Heart_Disease                     |heart murmur                     |Date                              |March 1998                       |Drug_Ingredient-Route    |Drug_Ingredient           |ACE inhibitors           |Route                     |p.o                      |
|1          |is_date_of               |Test                 |echocardiogram           |Date                 |March 1998               |is_date_of                |Test                              |echocardiogram                   |Date                              |March 1998                       |Drug_Ingredient-Frequency|Drug_Ingredient           |ACE inhibitors           |Frequency                 |daily                    |
|2          |is_finding_of            |Test                 |echocardiogram           |Heart_Disease        |left atrial enlargement  |is_finding_of             |Test                              |echocardiogram                   |Heart_Disease                     |left atrial enlargement          |Drug_Ingredient-Route    |Drug_Ingredient           |Furosemide               |Route                     |p.o                      |
|2          |is_result_of             |Test_Result          |normal                   |Test                 |left ventricular function|is_result_of              |Test_Result                       |normal                           |Test                              |left ventricular function        |null                     |null                      |null                     |null                      |null                     |
|2          |is_finding_of            |Test                 |left ventricular function|Heart_Disease        |left atrial enlargement  |is_finding_of             |Test                              |left ventricular function        |Heart_Disease                     |left atrial enlargement          |null                     |null                      |null                     |null                      |null                     |
|3          |Drug_Ingredient-Strength |Drug_Ingredient      |ACE inhibitors           |Strength             |10 mg                    |null                      |null                              |null                             |null                              |null                             |null                     |null                      |null                     |null                      |null                     |
|3          |Drug_Ingredient-Route    |Drug_Ingredient      |ACE inhibitors           |Route                |p.o                      |null                      |null                              |null                             |null                              |null                             |null                     |null                      |null                     |null                      |null                     |
|3          |Drug_Ingredient-Frequency|Drug_Ingredient      |ACE inhibitors           |Frequency            |daily                    |null                      |null                              |null                             |null                              |null                             |null                     |null                      |null                     |null                      |null                     |
|4          |Drug_Ingredient-Strength |Drug_Ingredient      |Furosemide               |Strength             |40 mg                    |null                      |null                              |null                             |null                              |null                             |null                     |null                      |null                     |null                      |null                     |
|4          |Drug_Ingredient-Route    |Drug_Ingredient      |Furosemide               |Route                |p.o                      |null                      |null                              |null                             |null                              |null                             |null                     |null                      |null                     |null                      |null                     |
+-----------+-------------------------+---------------------+-------------------------+---------------------+-------------------------+--------------------------+----------------------------------+---------------------------------+----------------------------------+---------------------------------+-------------------------+--------------------------+-------------------------+--------------------------+-------------------------+

Model Information

Model Name:	explain_clinical_doc_granular
Type:	pipeline
Compatibility:	Healthcare NLP 5.2.1+
License:	Licensed
Edition:	Official
Language:	en
Size:	1.7 GB

Included Models

DocumentAssembler
SentenceDetectorDLModel
TokenizerModel
WordEmbeddingsModel
MedicalNerModel
NerConverterInternalModel
NerConverterInternalModel
AssertionDLModel
PerceptronModel
DependencyParserModel
RelationExtractionModel
PosologyREModel
AnnotationMerger

PREVIOUSExplain Clinical Document - Oncology

NEXTExplain Clinical Document - Oncology