Summary and Schedule

OMOP Carpentries Course.

This course should provide clinicians and analysts with an introduction to the OMOP Common Data Model and how they can use R to access data and answer clinical questions.

The course is intended to be run over two days in person, or to be self directed online.

We suggest that learners are familiar with R and the tidyverse or do one of the carpentries introductory R courses.

Prerequisite

• A laptop with the current versions of the following installed:
  • the R software itself, and
  • RStudio Desktop.
• Download workshop.zip.

	Setup Instructions	Download files required for the lesson
Duration: 00h 00m	1. What is OMOP?	What is OMOP? Why is using a standard important in healthcare data? How do OMOP tables relate to each other? What are concept_ids and how can we get an humanly readable name for them?
Duration: 00h 00m	2. Exploring OMOP concepts with R	Find the vocabulary, domain and concept_class for a given concept_id Establish whether a concept_id is a standard concept Find all concepts within a given domain Find all concepts within a given vocabulary
Duration: 00h 00m	3. Parquet files	What is a parquet file? How to explore and open parquet files in R?
Duration: 00h 00m	4. More on concepts	Where to find other concept_ids in OMOP How to link OMOP tables
Duration: 00h 00m	5. Measurements and Observations	How to access measurements and observations ?
Duration: 00h 00m	6. Conditions and Visits	What are conditions in the OMOP CDM? When do we need to consider visits in our analysis?
Duration: 00h 00m	7. Medications	Where are medications stored ? How do you trace the relationship between concepts from different vocabularies?
Duration: 00h 00m	8. Dates and times	What
Duration: 00h 00m	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Setup instructions

Install R Packages

• install.packages(“dplyr”, verbose=FALSE)

• install.packages(“readr”, verbose=FALSE)

• install.packages(“purrr”, verbose=FALSE)

• install.packages(“CDMConnector”, verbose=FALSE)

• install.packages(“duckdb”, verbose=FALSE)

• install.packages(“lubridate”, verbose=FALSE)

• install.packages(“renv”, verbose=FALSE)

• install.packages(“arrow”, verbose=FALSE)

Create environment

1. Make a new folder in your Desktop called omop_course.
2. Download workshop.zip and move the file to this folder.
3. If it’s not unzipped yet, unzip it. There should now be a folders called workshop in the omop_course folder containing sub folders code and data.
4. You can access this folder from the Unix shell with:

BASH

$ cd
$ cd Desktop/omop_course/workshop