The University of Queensland OMOP Dataset

The University of Melbourne and The University of Queensland have signed an agreement to work on the conversion Queensland Health Cerner data to the OMOP common data model. Analysts are currently working on establishing a pilot extract load transform process (ETL) with synthetic Cerner data.

A community of practice is also being established to share expertise and support EMR conversions in other states.

 

Technical Meetings

We had our first EMR's to OMOP technical meeting today with colleagues from Queensland and NSW. 

We had demonstration of the OMOP ETL tool https://www.omop.link and a demonstration of Atlas. 

Extract, Transform, Load Framework for the Conversion of Health Databases to OMOP

Congratulations to our colleagues in UNSW on the publication of their paper on conversion methods for OMOP.

"Extract, Transform, Load Framework for the Conversion of Health Databases to OMOP"

Link:

https://www.medrxiv.org/content/10.1101/2021.04.08.21255178v2

EMR's to OMOP Progress

We are advancing work with two centres in Victoria and Queensland. Atlas is being set up in each centre with Synthetic CDM data to get researchers familiar with the structure of OMOP. All those R skills are going to come in handy!

https://www.ohdsi.org/atlas-a-unified-interface-for-the-ohdsi-tools/

Metadata is key to success

We had a really interesting meeting with Melanie Barlow and Julia Martin from the ARDC about metadata and Research Data Australia. We are planning how to describe the OMOP datasets. Fortunately OMOP already has a metadata table included in the CDM. 

https://ohdsi.github.io/CommonDataModel/cdm531.html#Metadata_Tables

ARDC Workshop

It's been a busy week on the EMR's to OMOP project. On Tuesday we had a workshop with ARDC to discuss sharing EMR to OMOP mappings in the future. Dr Daniel Capurro facilitated and we had a lively discussion of the issues. We are collating the results at the moment and will share the outcomes.

EMR's to OMOP

EMR's to OMOP is ARDC funded project that runs from 2021 - 2023. https://ardc.edu.au/project/electronic-medical-records-as-a-national-data-asset/

Hospital EMR data as a National Data Asset for Research (10.47486/PS014): This project aims to establish a national, research ready hospital electronic medical record (EMR) Data Asset that will enhance data accessibility for rapid interrogation and evidence generation. Data will be transformed to an international gold standard Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). 

Tools, mappings and experience gained will be made openly available, and a community of practice and a roadmap for continued national implementation will be built. The Data Asset will significantly improve the quality, accessibility and feasibility of EMR data warehouses by streamlining data governance, consent and ethics. The project’s outcome is a CDM platform, converting three Cerner-based data warehouses: Queensland Health ( State Public Health Hospital EMR), Austin Health and Western Health (Melbourne EMR). Learnings from the Cerner conversions will then be applied to the conversion of other data warehouse platforms including the EPIC EMR system which will be investigated in collaboration with the Peter MacCallum Cancer Centre.