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Day 1 · OMOP Common Data Model and Standardized Vocabularies

Welcome to Day 1 of the OHDSI Training Series!
Today we introduce the OMOP Common Data Model (CDM) — the foundation for all OHDSI analytics.
You’ll learn how data are organized, standardized, and queried using the OMOP vocabulary tables.

Objectives

By the end of this session, you should be able to: - Explain the purpose of the OMOP CDM and its standardized structure.
- Identify and describe core CDM tables (person, condition_occurrence, drug_exposure, etc.).
- Understand the role of vocabulary tables (concept, concept_relationship, concept_ancestor).
- Distinguish between standard vs non-standard concepts.
- Write basic SQL queries to explore OMOP data.
- Use the Athena vocabulary browser to find standard concepts.

Agenda

Time Topic
09:00 – 09:30 Welcome & Overview of OMOP CDM
09:30 – 10:30 Core Tables & Relationships
10:30 – 11:00 Break
11:00 – 12:00 Exploring the OMOP Vocabulary
12:00 – 13:00 Lunch
13:00 – 14:00 Hands-on: Querying Concepts with SQL
14:00 – 14:45 Demo: Using Athena
14:45 – 15:15 Recap & Discussion
15:15 – 15:30 Homework & Next Steps

Slides & Materials

File Description
Instructor Deck Full slide deck with speaker notes
Participant Workbook Workbook with fill-in exercises
Kahoot Quiz 10-question OMOP CDM quiz

Hands-on Activities

2. Query the concept Table

SELECT concept_id,
       concept_name,
       vocabulary_id,
       standard_concept
FROM concept
WHERE concept_name LIKE 'Major depressive disorder%';
Identify which are standard ('S') vs non-standard (NULL).

3. Map a Non-Standard Code to a Standard Concept

SELECT *
FROM concept_relationship
WHERE concept_id_1 = <nonstandard_id>
  AND relationship_id = 'Maps to';
Find the standard concept_id_2.

4. Explore Concept Relationships

SELECT cr.relationship_id,
       c.concept_name AS related_concept,
       c.domain_id
FROM concept_relationship cr
JOIN concept c ON cr.concept_id_2 = c.concept_id
WHERE cr.concept_id_1 = <standard_concept_id>;
- Look for “Is a,” “Subsumes,” and “Mapped from” relationships.
- Note hierarchical links for concept set creation.

Homework / Quiz Highlights

Check your understanding

The Day 1 self-check quiz and practice tasks are included in
Day 1 · Exercises.
Use the Cheat Sheet and
Day 1 Instructor Deck for reference.

See the slides and cheat sheet for full practice queries.

Suggested Reading

Instructor Notes

  • Demonstrate basic SQL queries live.
  • Encourage use of Athena to confirm concept IDs.
  • Remind learners that vocabularies update frequently — document versions.
  • Optional challenge: map ICD codes to SNOMED standards and compare results.

Module 0 · Environment Setup   Day 2 · Vocabulary & Data Quality

Day 1 lays the foundation for querying and interpreting standardized OMOP data. Day 2 will focus on concept sets, data quality, and SQL validation.