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OHDSI/OMOP Train-the-Trainer

A hands-on, multi-session curriculum for analysts, researchers, and trainers building expertise in the OHDSI ecosystem — from data model fundamentals to advanced analytics.

New here? Start with Feasibility First — is my question even answerable?

A 30-minute exemplar that takes the position of a researcher with a real question but no idea who to contact, what to ask, or whether the data can answer it. It walks from zero to a go/no-go decision on the public ATLAS demo, and it comes with a slide deck and script, a data-steward worksheet, and a checks-to-tools appendix.

Start Feasibility First Go straight to the go/no-go checklist

Start with Environment Setup Jump to Syllabus Slide Decks Companion Tools Find Your Learning Path

One ALS example runs through every session

The sessions use motor neuron disease, ALS medications such as riluzole, and the ALSFRS-R as their running example. The ALS use case page defines it and lists the concepts. A maternal and child health edition of this curriculum, with diabetes and pregnancy examples, is kept in a separate repository.

Program at a Glance

  • Core Sessions and Optional Sessions

    Build from OMOP CDM fundamentals through cohort building, data extraction, treatment pathways, and HADES analytics.

    View full syllabus

  • Hands-On Labs

    Sessions include guided SQL exercises and Atlas walkthroughs, and Days 1, 2, 3, 5, and 6 have Colab-ready Python notebooks with synthetic data.

    Browse exercises

  • Community & Support

    Weekly community meetings, open office hours, and a growing FAQ to support learners and trainers alike.

    Join the community

  • All Materials Included

    Slide kits, Jupyter notebooks, SQL cheat sheets, environment templates, and plain PowerPoint decks you can restyle.

    Downloads & Resources

The Curriculum

The program is organized in a deliberate sequence. Each session builds on the previous one — start at Day 0 (environment) and progress through the core four, then continue with the optional advanced sessions.

Core Track (Required)

Session Focus Module Exercise
Feasibility First — Is my question answerable? 30-min exemplar: from a raw question to a go/no-go decision Module Walkthrough · Checklist
Module 0 — Environment Setup Verify access to all tools and data Module Handout
Day 1 — OMOP Common Data Model CDM structure, tables, Athena vocabularies Module Exercise · SQL Snippets
Day 2 — Vocabulary & Data Quality Concept sets in Atlas, DQD, SQL validation Module Exercise
Day 3 — Cohort Definition Building and characterizing cohorts in ATLAS Module Exercise
Day 4 — Data Extraction Site-specific extraction and validation Module Exercise

Optional / Advanced Track

Session Focus Module Exercise
Day 5 — Treatment Pathways Sequence-of-care analysis in ATLAS Module Exercise
Day 6, Part 1 — HADES: Cohort Diagnostics and Feature Extraction R environment, cohort diagnostics, baseline covariates Module Exercise
Day 6, Part 2 — HADES: Patient-Level Prediction Prediction problem, model training, discrimination and calibration Module Exercise

How to Use This Site

For Participants

  1. Complete Module 0 before anything else — verify your tool access at least 48 hours before Day 1.
  2. Follow the core track in order. Each day's module has an agenda, objectives, slides, and a matching exercise.
  3. Use the Common Artifacts for cheat sheets, SQL templates, and the environment checklist.
  4. Notebooks cover Days 1, 2, 3, 5, and 6. Those exercise pages have a Colab badge, so you can run them with synthetic data even without CDM access. Day 4 has no notebook because extraction is site specific.

For Trainers

  1. Fork this repository and fill in site-specific details (warehouse, SQL client, ATLAS URL) in the Day 4 module and Environment pages.
  2. Use the plain template from the Downloads & Resources page for any new decks, and apply your own theme if you want one.
  3. Instructor notes are embedded (collapsed) in each exercise page — expand them before your session.
  4. Host community meetings using the Community pages as a template.

Sample Schedule

This schedule reflects one delivery of the program. Each session is a half day (about 3.5 hours). Day 6 is now taught as separate sessions, Part 1 and Part 2, each a half day.

Session Suggested Date Focus
Environment Walk-through Fri, Oct 31 · 12:00–1:00 Access check for data and tools
Day 1 — OMOP Common Data Model Fri, Nov 7 · 9:30–1:00 Schema, key tables, Athena
Day 2 — Vocabulary & Data Quality Fri, Nov 14 · 9:30–1:00 Concept sets, DQD principles
Day 3 — Cohort Definition w/ ATLAS Fri, Nov 21 · 9:30–1:00 Cohorts and characterization
Day 4 — Data Extraction Tools Mon, Dec 1 · 9:30–1:00 Build analytic datasets
Post-training Q&A Fri, Dec 12 · 11:30–1:00 Q&A, next steps
Day 5 (Optional) — Treatment Pathways Fri, Jan 9 · 9:30–1:00 Sequences of care
Day 6 (Optional) — HADES Fri, Jan 16 · 9:30–1:00 R-based analytics framework

Common Artifacts

These shared resources are used across multiple sessions:

  • Environment Setup Handout

    One-page pre-session participant checklist.

    View handout

  • OMOP Vocabulary & SQL Cheat Sheet

    Key queries for concepts, ancestors, cohort counts, and more.

    View cheat sheet

  • SQL Validation Mini Lab

    Step-by-step guide: export Atlas SQL, validate in your client, compare outputs.

    Open lab

  • Environment Checklist Template

    Trainer-ready checklist to track participant readiness per tool.

    Download template

All content in docs/ is version-controlled. Updates and new contributions are tracked automatically via the GitHub repository.