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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 Mike

Presentation: HERON ETL for i2b2 and Discussion on how we might support reproducible science as a community


Mike Mendis, Partners HealthCare – i2b2

 

 

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Session Summary:

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.

 


 

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Presentations (5)

 

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i2b2FoundationUpdate
i2b2FoundationUpdate
i2b2 Foundation Update

 

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

 

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etlEpic-Campbell
etlEpic-Campbell
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

 

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etlEureka-post
etlEureka-post
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

 

 

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etlHeron-Waitman
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

 

 

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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

https://github.com/kumc-bmi

 

Info Box
titleAccess 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.

 

 

 


 

 

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etlBI-Mike
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

 

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