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? What information would you expect to find in the person table? What information would you expect to find in the condition_occurrence table? How can you join these tables to aggregate information?
Duration: 00h 00m	2. Why OMOP?	Why use OMOP? Why not use spreadsheets? What are the advantages of OMOP? What are the disadvantages of OMOP?
Duration: 00h 00m	3. concepts and conditions	What is an OMOP concept ? Where are patient conditions stored in OMOP ?
Duration: 00h 00m	4. measurements and observations	How to access measurements and observations ?
Duration: 00h 00m	5. Visits	What are visits and how can they be used ?
Duration: 00h 00m	6. Medications	Where are medications stored ?
Duration: 00h 00m	7. Community provided software for working with OMOP data	What are some of the R tools that can work on OMOP CDM instances ?
Duration: 00h 00m	8. Placeholder Chapter 8	What
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