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The PEDSnet Data Quality Assessment Toolkit (OMOP CDM)
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Data Quality Assessment in PEDSnet


This toolkit has been designed for conducting data quality assessments on clinical datasets modeled using the OMOP common data model. The toolkit includes a wide variety of data quality checks and a GitHub-based issue reporting mechanism. The toolkit is being routinely used by the PEDSnet CDRN.


  • Data: the data quality catalog of checks, summaries of previous data cycle, and acceptable valuesets for various fields.
  • Doc: documentation and set up instruction for the program
  • Infrastructure: constants and internal helper functions
  • Library: contains data quality checks and utility functions
  • Main: single and multi-variable data quality scripts
  • Resources: configuration file
  • Tools: scripts for GitHub-based feedback generation

Required Downloads


Java version 5

If using OSX, download here

Note: version 5 must be installed, even if a higher version of Java is installed


R version 3.1.x or above, 64-bit (Comprehensive R Archive Network)

R Packages

"dbplyr","lubridate", "tictoc", "testthat", "data.table"))

  • Minimum Versions Required:
    • R: 3.2
    • DBI: 0.7
    • dplyr: 0.7
    • dbplyr: 1.2
    • readr: 1.1
    • rlang: 0.1.4
    • stringr: 1.2
  • The RPostgres package is not required if PostgreSQL is not the target database type
  • For Oracle users, the ROracle package should be installed

For troubleshooting with install_github("ohdsi/SqlRender"), please see here.

Note: if previously installed, run update.packages() to get the latest version of each library

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