Have you wondered how to use large standardized datasets such as the national All of Us: Precision Medicine Research Program (https://www.researchallofus.org/data-tools/workbench/) or your own academic medical center research data warehouse to answer your clinical and healthcare research questions? Many of these datasets are built on the OMOP (Observational Medical Outcomes Partnership) common data model. A first step to being able to conduct a study using these types of real-world data is to understand this standard and accompanying tools and strategies for accessing, querying, and analyzing OMOP data.
This year we offer a one-time Spring Workshop on Common Data Models for Real-world Data. This training focuses on the OMOP common data model and its application to real-world datasets. OMOP is governed by the Observational Health Data Sciences and Informatics (or OHDSI, pronounced “Odyssey”) program which is an international, multi-stakeholder, interdisciplinary collaborative to bring out the value of health data through large-scale analytics. This training will allow clinical investigators, graduate students and fellows, analysts, and programmers to conduct large scale observational research using registry and electronic health records data.
Priority registration for the Spring Workshop is offered to individuals affiliated with the institutions that participate in pSCANNER, R2D2, and SYSU/FAH. The Spring Workshop will be held virtually, March 5 – March 26. The training will be conducted by IQVIA.
2021 Program Chair: Dr. Katherine Kim, University of California Davis, and Dr. Haibo Wang, Sun Yat-sen University/First Affiliated Hospital. Direct any questions to personalizedhealth@ucdavis.edu
This training is provided at no cost through the generous support of the Lingnan Foundation.
Full Workshop Series (Sold Out)
Add yourself to the Full Workshop Waitlist here (Closed)
Register for Introduction for Clinical Investigators (session 1 only) (Sold Out)
Note: participants will receive confirmation when their registration is approved.
Spring Workshop Schedule March 2021
This is an intensive program conducted on four Fridays in March in the US (Pacific Standard Time) and four Saturdays in March in China (China Standard Time). The sessions are described below. Attendees for session 1 are not required to attend subsequent sessions. However, attendees who wish to attend sessions 2-4 must attend session 1 and complete the required homework prior to session 2.
SESSION 1 – Intro to OHDSI / OMOP for Clinical Investigators (4 hours)
Session 1 Slides: OHDSI Introduction
Session 1 Video: UC Systems OMOP Training Session 1
This is an introductory session for PIs or investigators who want an overview of these topics: OHDSI research steps, high level introduction of OHDSI tools, concept-set expressions, and introduction to Atlas. Attendees for this session are not required to attend subsequent sessions.
California US, PST (Friday, Mar 5) 9:00am-1:00pm. Virtual in English
Guangzhou, China, CST (Saturday, Mar 6) 9:00am-1:00pm. Virtual in Chinese
Homework prior to session 2 (8 hours):
This is mandatory for attendees of sessions 2-4. To help you get through the exercises, we ask you to complete the following homework prior to session 2.
- Read Chapter 4 and 5 in The Book of OHDSI
- Listen to the last year’s recording here
OR
- Listen to the CDM/Vocabulary class on EHDEN Academy
SESSION 2 – Common Data Model and Standardized Vocabulary (8 hours)
Session 2 Slides: OMOP CDM Vocabulary Tutorial
Session 2 Video: UC Systems OMOP Training Session 2
Attendance at previous sessions and completion of the homework is a prerequisite. Topics include: OMOP CDM V5 standard (data structure, content, conventions), structure and content of the OHDSI vocabularies, OMOP Standardized Vocabularies relationships, concept-set expressions, and introduction to Atlas
California US, PST (Friday, Mar 12) 9:00am-5:00pm. Virtual in English
Guangzhou, China, CST (Saturday, Mar 13) 9:00am-5:00pm. Virtual in Chinese
SESSION 3a – Leveraging the OHDSI Ecosystem as a Developer, US Only (8 hours)
Session 3 Slides: Leveraging the OHDSI ecosystem as a developer
Session 3 Homework: HERE
Session 3 Video: UC Systems OMOP Training Session 3
Attendance at previous sessions and completion of the homework is a prerequisite. Topics include: Principles for cohort definition and evaluation, rule-based heuristics in ATLAS, use of OMOP hierarchy in research, cohort definitions applied to analytical use cases of: disease phenotyping, exposure definition, and clinical trial feasibility, and study design and develop using OHDSI tool
California US, PST (Friday, Mar 19) 9:00am-5:00pm. Virtual in English
SESSION 3b – ETL Development, China Only (8 hours)
Attendance at previous sessions and completion of the homework is a prerequisite. Topics include: Running through ETL analysis tools for data source profile, ETL specification, and vocabulary mapping, use of source control, use of different ETL environments, design of ETL scripting, and use of data quality tools and scripts
Guangzhou, China, CST (Saturday, Mar 20) 9:00am-5:00pm. Virtual in Chinese
Session 4: Leveraging the OHDSI Ecosystem to run OHDSI Network Studies (8 hours)
Session 4a Slides: Leveraging the OHDSI ecosystem to run Network Studies
Session 4b Slides: OMOP ETL Conversions
Session 4 Video: UC Systems OMOP Training Session 4
Attendance at previous sessions and completion of the homework is a prerequisite. Topics include: Using a study question, build the study using Atlas, SQL or R, and running the study within Astellas environments
California US, PST (Friday, Mar 26) 9:00am-5:00pm. Virtual in English
Guangzhou, China, CST (Saturday, Mar 27) 9:00am-5:00pm. Virtual in Chinese
When your registration is approved, you will be sent links to tutorials and materials on foundational concepts such as Common Data Model and Standardized Vocabularies.