i2b2 Community Discussion at AMIA: i2b2 and ETL Processes
Date: November 14, 2016
Presenters:
Diane Keogh, Managing Director, i2b2 Foundation
Presentation: i2b2 Foundation Update
James R. Campbell, MD, University of Nebraska
Presentation: Enhancing interoperation: an i2b2 ETL schema for Epic EHRs
Andrew Post, MD, PhD, Atlanta Clinical & Translational Science Institute (ACTSI)
Presentation: i2b2 ETL - Eureka Clinical Analytics Project at Emory University
Russ Waitman, PhD, University of Kansas Medical Center
Presentation: HERON ETL for i2b2 and Discussion on how we might support reproducible science as a community
Mike Mendis, Partners HealthCare – i2b2
Presentation: ETL with Business Intelligence Development Studio (BIDS)
Session Summary
The second i2b2 Educational Seminar was held on November 14, 2016 at the AMIA Conference in Chicago, IL. The main topic of this educational seminar was a community discussion around i2b2 and ETL processes. Several community members presented information about their experience using ETL tools with their EMR and i2b2. These discussions evolved into how the community can share the ETL scripts with the rest of the community.
Presentations (5)
Presenter: Diane Keogh, Managing Director, i2b2 Foundation
Discussion Highlights:
- Accomplishments to date
- Source code repositories
- Sharing i2b2 plugins
- Community Support Efforts – Educational webinar series
- Exploring partnership between i2b2 and tranSMART foundations
Presentation Slides
Enhancing interoperation: an i2b2 ETL schema for Epic EHRs
Presenter: James R. Campbell, MD, University of Nebraska
Discussion Highlights:
- ETL Library for Epic EHRs
- Organizing i2b2 for interoperation
- i2b2 ETL architecture for Epic EHRs
- Data warehouse extracts vs CCDA vs FHIR interface for transportability of code
Presentation Video
Presentation Slides
i2b2 ETL - Eureka Clinical Analytics Project at Emory University
Presenter: Andrew Post, MD, PhD, Atlanta Clinical & Translational Science Institute
Discussion Highlights:
- ETL tools used to load from central warehouse into i2b2
- EMR is Cerner
- Implemented incremental loading
Presentation Video
Presentation Slides
HERON ETL for i2b2 and Discussion on how we might support reproducible science as a community
Presenter: Russ Waitman, PhD, University of Kansas Medical Center
Discussion Highlights:
- HERON ETL Data Flow
- Jenkins used to automate the ETL process
- Data Sources:
- REDCap
- Clarity
- IDX
- University Health system consortium data
Presentation Video
Presentation Slides
Additional Resources
KUMC maintains overview of our HERON ETL process here:
https://informatics.kumc.edu/work/wiki/HERON
Links to an older code repository:
https://informatics.kumc.edu/work/browser/heron_load
Through our work with the GPC we are now maintain our current code repository on Github
Access to Repository
The actual HERON ETL is in a private project https://github.com/kumc-bmi/heron. Once you have a GitHub account, contact Dan Connolly and Heron-Admin@kumc.edu to get access to the latest code.
ETL with Business Intelligence Development Studio (BIDS)
Presenter: Mike Mendis, Partners HealthCare – i2b2
Discussion Highlights:
BIDS is Visual Studio development environment
Microsoft offers SQL Server and Business Intelligence stack provides
- SQL Server / T-SQL query engine
- Integration Services provide ETL tools
- Analysis Services provides tools to build multidimensional databases…
- Reporting Services provides tools to build reports and a portal to deploy reports
i2b2 ETLsMicrosoft Connectors available for Oracle database support
- Can be used to populate i2b2 data marts
- Run stored procedure to convert to standard format
Presentation Video
Presentation Slides
