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OMOPCDMCohortCreator

Dev Test Coverage Zulip Build Status Code Style: Blue DOI

Create cohorts from databases utilizing the OMOP CDM.

This is a work in progress package that allows one to interface with an OMOP CDM database for observational health research and analytics. This package works on version 5.4 of the OMOP CDM and provides a number of filters and getter functions.

For questions, feel free to start a discussion, create an issue, or post on Zulip.

This package uses a functional approach to query databases in the OMOP Common Data Model format whereby you could build rapidly lines of inquiry into the database. Furthermore, this package is a companion to those tools found in the HADES ecosystem. Documentation has been set up so please check them out! To get started, visit the Tutorials section as well as visit the API section to see all the functions available. If you want to contribute, please check out our Contributing guide!

Main Features 🔧

The biggest features of this package are:

  • Incremental building blocks for creating an analysis pipeline in the form of (more information in API):
    • "Getter" functions to "get" information from a database
    • "Filter" functions to "filter" information from a database
    • "Generator" functions to "generate" database information and connections
    • "Executor" functions to "execute" on retrieved information
  • Automatic targeting and support for the SQL flavors (via FunSQL.jl):
    • postgresql
    • sqlite
    • redshift
  • Prepare SQL queries if unable to connect to database via OMOPCDMCohortCreator that could then be run on a given SQL database directly
  • Does not mutate database or require temp tables
  • Interoperable with the R language via JuliaConnectoR to work directly within R syntax (see Tutorials)
  • Readily parallelizable via Distributed.jl
  • Complementary to OHDSI HADES ecosystem tools
  • Extensive test suite to ensure correctness and compliance with privacy preserving methods (HITECH, etc.)

Maintainership 👷

This package is currently maintained by Jacob S. Zelko (AKA @TheCedarPrince) as of October 2022. If this repository should fall out of maintainership and there is an urgent need, please contact members of the JuliaHealth organization for assistance. Thank you!

Citation Information 📝

@software{Zelko_OMOPCDMCohortCreator_0_2_0_2022,
author = {Zelko, Jacob and Chinta, Varshini},
doi = {10.5281/zenodo.7052105},
month = {10},
title = {{OMOPCDMCohortCreator 0.2.0}},
version = {0.2.0},
year = {2022}
}