N3C Short Course, June 2022

Educational material for the N3C short course, June 2022. (All assignments are contained in the secure Enclave.)

Material Online

Background

• Protecting N3C Data: an important list of rules to follow to protect patient data. In short, keep everything in the Enclave and use the data only for projects that are specifically approved. Please read this carefully.

• Analytical Tools: To be productive in the N3C Enclave during this short course, we recommend that you (a) are comfortable with basic SQL and (b) know at least a little Python or R.

• Assets: A running list of the links that that might be helpful references in the future.

• Syllabus

Daily Sessions

Session 1

• Study Design & Project Planning Or: How N3C Researchers (Try to) Organize Their Work, by Harold Lehmann.
• Navigating Foundry by Shawn O'Neil
• Concept Set Curation by Shawn O'Neil
• Intro to Code Workbook Training Module by Shawn O'Neil
  • This 31 minute training module video covers everything we covered in class today and more. It also introduces using templates from the Knowledge Store, though the template search interface has changed since the recording.
• Assignment: see pages 4-5 in the Syllabus (link above)

Session 2 (optional)

• Office Hours and Open Discussion
• Assignment: same as Session 1

Session 3

• Overview of UNMC's Malnutrition Study (and pptx) by Jana Ponce and Jerrod Anzalone
• Session 3 Slides (and pptx) by Jerrod Anzalone
• Session 3 Exercises & Homework (and docx) by Jerrod Anzalone
• CSV containing Malnutrition Concept Sets
• Session 3 Solutions to Exercises

Session 4

• Data Analysis (and pptx) by Jerrod Anzalone
• Data Validation by Will Beasley
• Data Visualization by Will Beasley

Assets

• Google Drive directory

Agenda