Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Health Information Technology and Healthcare Information System01:30

Health Information Technology and Healthcare Information System

971
Health Information Technology (HIT)
Health Information Technology, commonly called HIT, integrates advanced information systems and technology in healthcare settings. Its primary functions include:
971
Purpose of Health Records II01:19

Purpose of Health Records II

1.0K
Health records serve various essential purposes in the healthcare system. Here are some key purposes:
1.0K
Integrated Healthcare System01:20

Integrated Healthcare System

1.8K
An integrated healthcare system (IHS) is a set of organizations that provides for or arranges to provide coordinated and continuous service to a defined population. The IHS takes responsibility for that particular population's health status and outcome, both clinically and fiscally. An integrated healthcare system is a well-organized, well-coordinated, and collaborative network. The integrated delivery system is a network that connects different healthcare providers to deliver organized,...
1.8K
Issues And Trends In Healthcare Delivery System01:29

Issues And Trends In Healthcare Delivery System

5.9K
The issues and trends in healthcare delivery are constantly changing. The COVID-19 pandemic is one recent issue that wreaked havoc on healthcare systems, causing a shortage of healthcare workers, high demand for medicines and supplies, and increased medical expenditure due to a lack of insurance. Other issues include rising healthcare costs and care fragmentation.
Cost Containment
Payment for healthcare services has historically promoted adoption of costly and often unnecessary or inefficient...
5.9K
Purpose of Health Records I01:11

Purpose of Health Records I

1.4K
The vital purpose of health records is to provide a complete and accurate account of a patient's medical history, including communication, diagnostic and therapeutic orders, care planning, research, and quality review.
Here's a breakdown of how health records serve these purposes:
1.4K
Methods of Documentation VII: EMR01:30

Methods of Documentation VII: EMR

934
Electronic Medical Records (EMRs) primarily center around electronically documenting patients' health information within a single healthcare organization or practice. They contain essential clinical data related to a patient's medical history, diagnoses, medications, treatment plans, lab results, and other pertinent information relevant to the specific encounter or episode of care. EMRs are designed to streamline documentation and workflow processes within individual healthcare...
934

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Medically Assisted Reproduction and Hormone-Related Cancers.

JAMA network open·2026
Same author

Deep learning in the early diagnosis of acute aortic dissection.

Frontiers in cardiovascular medicine·2026
Same author

CUI-Curate: a GraphRAG-based framework for automated clinical concept curation for NLP applications.

Journal of the American Medical Informatics Association : JAMIA·2026
Same author

Immediate versus delayed free-flap breast reconstruction: Higher readmission after immediate reconstruction in a 20,415-patient IPTW NSQIP cohort.

Journal of plastic, reconstructive & aesthetic surgery : JPRAS·2026
Same author

AI-Based Prediction of Clinical Deterioration in Hospitalised Cardiac Patients.

Studies in health technology and informatics·2026
Same author

Limits of Generative Pre-Training in Structured EMR Trajectories with Irregular Sampling.

Studies in health technology and informatics·2026

Related Experiment Video

Updated: Sep 27, 2025

Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts
08:51

Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts

Published on: September 20, 2024

1.5K

Extract, transform, load framework for the conversion of health databases to OMOP.

Juan C Quiroz1, Tim Chard1, Zhisheng Sa1

  • 1Centre for Big Data Research in Health, UNSW, Sydney, Australia.

Plos One
|April 11, 2022
PubMed
Summary

We developed a metadata-driven ETL framework to simplify mapping health data to the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM). This tool streamlines data conversion for reproducible, large-scale research.

More Related Videos

Executing Complexity-Increasing Queries in Relational MySQL and NoSQL MongoDB and EXist Size-Growing ISO/EN 13606 Standardized EHR Databases
07:26

Executing Complexity-Increasing Queries in Relational MySQL and NoSQL MongoDB and EXist Size-Growing ISO/EN 13606 Standardized EHR Databases

Published on: March 19, 2018

9.5K
TBase - an Integrated Electronic Health Record and Research Database for Kidney Transplant Recipients
09:00

TBase - an Integrated Electronic Health Record and Research Database for Kidney Transplant Recipients

Published on: April 13, 2021

4.8K

Related Experiment Videos

Last Updated: Sep 27, 2025

Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts
08:51

Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts

Published on: September 20, 2024

1.5K
Executing Complexity-Increasing Queries in Relational MySQL and NoSQL MongoDB and EXist Size-Growing ISO/EN 13606 Standardized EHR Databases
07:26

Executing Complexity-Increasing Queries in Relational MySQL and NoSQL MongoDB and EXist Size-Growing ISO/EN 13606 Standardized EHR Databases

Published on: March 19, 2018

9.5K
TBase - an Integrated Electronic Health Record and Research Database for Kidney Transplant Recipients
09:00

TBase - an Integrated Electronic Health Record and Research Database for Kidney Transplant Recipients

Published on: April 13, 2021

4.8K

Area of Science:

  • Health Informatics
  • Data Standardization
  • Observational Health Data Sciences and Information (OHDSI)

Background:

  • Common data models like the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) are crucial for data standardization, reproducibility, and large-scale health studies.
  • Converting diverse health datasets to the OMOP CDM is a complex, time-consuming, and resource-intensive process.
  • There is a significant need for efficient tools to facilitate the mapping of data to the OMOP CDM.

Purpose of the Study:

  • To propose a novel, metadata-driven Extract, Transform, Load (ETL) framework designed for generic application across various source health datasets.
  • To develop a new data manipulation language (DML) that organizes SQL snippets within YAML files for intuitive mapping logic.
  • To provide a web-based application for users to easily manage mapping logic and generate ETL scripts for OMOP CDM conversion.

Main Methods:

  • Developed a metadata-driven ETL framework that utilizes a novel data manipulation language (DML) structured in YAML.
  • Implemented a compiler to translate YAML-defined mapping logic into executable ETL scripts.
  • Created a web application with an integrated editor for uploading, editing, and managing YAML files, generating SQL ETL scripts.

Main Results:

  • The proposed framework offers a generic and metadata-driven approach to ETL processes for OMOP CDM data mapping.
  • The DML enhances readability, refactoring, and maintainability of ETL scripts, reducing technical debt.
  • The web application provides a user-friendly interface for managing mapping logic and generating standardized ETL SQL scripts.

Conclusions:

  • The developed ETL framework and DML significantly streamline the process of mapping diverse health datasets to the OMOP CDM.
  • The framework promotes transparency and reusability of mapping processes across different institutions, fostering collaborative research.
  • This tool addresses the critical need for efficient data conversion, enabling broader participation in large-scale observational health studies.