Syllabus — OHDSI Train-the-Trainer (6-Week Core + Optional Modules)
This master syllabus outlines the required readings, tools, and assignments for the six-week OHDSI Train-the-Trainer program, along with optional advanced modules for continued professional development.
The program bridges Epic Clarity experience with OMOP/OHDSI skills through both GUI-based (Atlas, Athena) and SQL-based (Databricks, DBeaver) learning.
A) Core Six-Week Syllabus (Required)
Tip: Chapters refer to the Book of OHDSI.
For broader context on data sources and study design, see the RWD Guide.
| Week / Day | Focus | Primary Readings / Viewings | Tools & Docs | Homework / Follow-up |
|---|---|---|---|---|
| Day 0 – Environment Setup | Verify access and installations | OHDSI.org – Who We Are · OHDSI Forum “Introduce Yourself” | Environment Checklist Template · ATLAS login · SQL client setup (Databricks / DBeaver) | Complete environment checklist · Test CDM connection and ATLAS login |
| Week 1 – OMOP CDM & Athena Vocabulary Exploration | Understand CDM structure and vocabularies | Book of OHDSI Ch. 4 The Common Data Model (§ 4.1 Design Principles · 4.2 Data Model Conventions · 4.3 CDM Standardized Tables); Ch. 5 Standardized Vocabularies (§ 5.1 Why Vocabularies and Why · 5.2 Concepts · 5.3 Relationships · 5.4 Hierarchy) | Athena Browser · Example CDM entity–relationship diagram (ERD) | Identify standard and non-standard concepts in Athena · Document mappings (Maps to, Is a, Has ancestor) |
| Week 2 – Concept Sets in Atlas & Introduction to Data Quality Concepts (with SQL Validation) | Build concept sets in Atlas and validate them using SQL tools | Book of OHDSI Ch. 4 (Data Quality Concepts Overview) | Atlas Concept Sets · SQL Clients (Databricks / DBeaver) · OMOP SQL Examples | Export Atlas SQL for concept sets · Run and validate logic in Databricks/DBeaver · Reflect on vocabulary mapping and data quality concepts |
| Week 3 – Cohort Definition & Characterization with ATLAS (SQL Exploration) | Design and characterize cohorts; explore cohort SQL | Book of OHDSI Ch. 19 (Study Steps) | ATLAS Cohort Editor · Characterization Module · SQL Clients | Export cohort SQL from Atlas · Annotate key joins and logic in SQL client · Compare table usage across OMOP domains |
| Week 4 – Data Extraction with SEARCH & SQL Validation | Retrieve OMOP data for analysis and cross-check results | Book of OHDSI Ch. 3 (ETL Processes) | SEARCH Tool · Databricks / DBeaver · OMOP SQL Examples | Re-run SEARCH extraction SQL manually in Databricks/DBeaver · Validate counts and compare results |
| Week 5 – Treatment Pathway Analysis (Optional) | Sequence treatments and visualize pathways | Book of OHDSI Ch. 12 (Estimation) | ATLAS Pathways · Pathway Analysis Docs | Generate and interpret pathway plots · Summarize one analytical insight |
| Week 6 – Advanced Analytics with HADES (Optional) | Characterization / Estimation / Prediction pipelines | Book of OHDSI Ch. 13 (Prediction) & Ch. 14 (HADES) | HADES R Packages | Execute a small HADES workflow and report diagnostics |
B) Optional / Advanced Modules (Beyond 6 Weeks)
These modules are not part of the six-week course but can be assigned for continued self-study.
| Module # | Topic | Primary Readings | Key Tools / Docs | Optional Context / Use Case |
|---|---|---|---|---|
| 7. Team Building & Project Management | Cross-functional teamwork in OHDSI | Book of OHDSI Ch. 15 (Community) | GitHub best practices · Agile boards | Managing multi-site collaborations |
| 8. Advanced Topics | ML, NLP, FHIR, unstructured data | Book of OHDSI Ch. 14 (HADES) | NOTE_NLP · FHIR mapping guides | Extending OMOP to AI and interoperability |
| 9. Train-the-Trainer Skills | Adult learning and facilitation | Adult learning primers · Presentation skills | EXCELERATE TtT materials | Designing your own institutional training program |
| 10. Capstone Project | End-to-end practice study | Revisit Ch. 12, 13, 19 | ATLAS export → SQL / R | Present a mini reproducible study |
| 11. Wrap-Up & Next Steps | Sustaining engagement | Book of OHDSI Ch. 15 (Community) | OHDSI Workgroups Directory | Join or lead community workgroups |
| 12. Refresher (3-Month Post-Course) | Review and updates | Book of OHDSI Ch. 19 (Study Steps) | Latest OHDSI release notes | Continuing learning & updates |
C) Persona-Based Study Paths (Quick Reference)
| Persona | Core Modules | Key Tools | Suggested Extras |
|---|---|---|---|
| Vocabulary / Terminology Experts | Weeks 1–3 | Athena · Atlas Concept Sets · SQL Clients (Databricks/DBeaver) | White Rabbit / Rabbit-in-a-Hat |
| Statisticians / Data Analysts | Weeks 3–6 (optional) | Atlas Pathways · HADES · SQL review of outputs | RWD Guide (bias/confounding) |
| Data Engineers (SQL-first) | Weeks 2–4 | Databricks · DBeaver · SEARCH · DatabaseConnector | Build reproducible pipelines in GitHub |
| Clinicians / Analysts | Weeks 1–3 | Athena · Atlas Cohort Editor | Explore cohort outputs and characterization summaries |
D) Key Supplemental Resources
| Resource | Purpose / Description |
|---|---|
| Environment Checklist Template | Validate all required system access before Week 1. |
| OMOP SQL Examples | Common SQL patterns for exploring concepts, ancestors, and cohort logic in Databricks or DBeaver. |
| SQL Validation Mini Lab | Step-by-step guide to export Atlas SQL, run validation queries, and compare outputs. |
| Book of OHDSI | Core text for OMOP CDM and OHDSI methods. |
| RWD Guide | Companion text for understanding bias, confounding, and data quality. |
E) How to Use
- Before class: Read the assigned Book of OHDSI chapters and open the listed tools.
- During class: Use both Atlas/Athena and your SQL client for guided exercises.
- After class: Complete weekly homework and optional SQL validation tasks.
- As a trainer: Bookmark these core references and update your repo with local connection instructions.
This syllabus supports the revised six-week OHDSI Train-the-Trainer program and provides a bridge between graphical and SQL-based workflows.