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

This lesson assumes you have current versions of the following installed on your computer:

• the R software itself, and
• RStudio Desktop.

You also need to download some files to follow this lesson:

• Download omop-data.zip.

TODO: update this file with download requirements for the whole course.

	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 and domain 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. More on concepts	Where to find other concept_ids in OMOP How to link OMOP tables
Duration: 00h 00m	Finish

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

This lesson assumes you have current versions of the following installed on your computer:

1. the R software itself, and
2. RStudio Desktop.

You also need to download some files to follow this lesson:

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

BASH

$ cd
$ cd Desktop/omop_taster/data