[ANN] OMOPCDMCohortCreator.jl v0.2.0 - Docs, Tests, Features Oh My!

TheCedarPrince
Mon, 24 Oct 2022 05:11:39 +0000
Package Announcements

Hi everyone,

It is with pride that my colleagues and I announce the release of OMOPCDMCohortCreator.jl 0.2.0! Some of the biggest updates are that:

The documentation has received a massive update with fantastic new tutorials, an updated API guide and a new contributing section if you want to get involved!

SQL export has been added to support the creation of prepared SQL statements that can run against an OMOP CDM database in situations where adding software within the database environment (such as Julia or other packages) is not feasible or supported. Example:

# Five patients with strep throat
strep_patients = [283.0, 326.0, 579.0, 334.0, 559.0]

# Age groups that we will use to bucket patients' ages into
age_groups = [[0, 4], [5, 9], [10, 14], [15, 19], [20, 24], [25, 29], [30, 34], [35, 39], [40, 44], [45, 49], [50, 54], [55, 59], [60, 64], [65, 69], [70, 74], [75, 79], [80, 84], [85, 89], [90, 94], [95, 99]]

# Return the prepared SQL statement
GetPatientAgeGroup(strep_patients; age_groupings = age_groups)

Which returns a prepared SQL statement like this:

SELECT
  "PERSON_2"."person_id",
  (CASE WHEN ("PERSON_2"."age" < 5) THEN '0 - 4' WHEN ("PERSON_2"."age" < 10) THEN '5 - 9' WHEN ("PERSON_2"."age" < 15) THEN '10 - 14' WHEN ("PERSON_2"."age" < 20) THEN '15 - 19' WHEN ("PERSON_2"."age" < 25) THEN '20 - 24' WHEN ("PERSON_2"."age" < 30) THEN '25 - 29' WHEN ("PERSON_2"."age" < 35) THEN '30 - 34' WHEN ("PERSON_2"."age" < 40) THEN '35 - 39' WHEN ("PERSON_2"."age" < 45) THEN '40 - 44' WHEN ("PERSON_2"."age" < 50) THEN '45 - 49' WHEN ("PERSON_2"."age" < 55) THEN '50 - 54' WHEN ("PERSON_2"."age" < 60) THEN '55 - 59' WHEN ("PERSON_2"."age" < 65) THEN '60 - 64' WHEN ("PERSON_2"."age" < 70) THEN '65 - 69' WHEN ("PERSON_2"."age" < 75) THEN '70 - 74' WHEN ("PERSON_2"."age" < 80) THEN '75 - 79' WHEN ("PERSON_2"."age" < 85) THEN '80 - 84' WHEN ("PERSON_2"."age" < 90) THEN '85 - 89' WHEN ("PERSON_2"."age" < 95) THEN '90 - 94' WHEN ("PERSON_2"."age" < 100) THEN '95 - 99' END) AS "age_group"
FROM (
  SELECT
    "PERSON_1"."person_id",
    (2022 - "PERSON_1"."year_of_birth") AS "age"
  FROM "PERSON" AS "PERSON_1"
  WHERE ("PERSON_1"."person_id" IN (283.0, 326.0, 579.0, 334.0, 559.0))
) AS "PERSON_2"

A few different SQL flavors are supported at the moment but the generated SQL matches ANSI SQL standards as closely as possible.

Thanks to the excellent work done by @stefan-m-lenz in JuliaConnectoR, there is now a tutorial that shows how to use OMOPCDMCohortCreator within R – very minimal Julia knowledge required!

An extensive testing suite has been added in this version to ensure correctness and compliance with privacy preserving methods for patient data.

To see the full number of new features, check out the changelog!

The particular use of this tool is going to be highlighted in a forthcoming JuliaCon Proceedings paper as well and I was able to present on results from this package at a recent conference where I showed work on health disparities. We will continue pushing forward this tool and if there is any features you need or questions, please let me know!

Thank you!

~ tcp

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