curioustauseef / tutorial-etl

Course materials for OHDSI ETL tutorial

Tutorial-ETL

Materials necessary for the "OMOP Common Data Model Extract, Transform & Load Tutorial". The goal of this tutorial is to learn about best practices and OHDSI tools developed to help with designing an extract, transform, & load process to take your database from raw observational data to the OMOP Common Data Model. Pre-requisite course would be the OMOP CDM & Vocabulary Tutorial or working experience with the OMOP CDM and OMOP Vocabulary.

Pre-Reads

• Lauren's Story (Endometriosis UK)
• Synthea Data Dictionary
• ETL - Book of OHDSI (OPTIONAL)

Materials for Students

• PowerPoint
• Synthea ETL Document (for tutorial)

Tutorial Materials

• Synthea ETL
• Synthea ETL Document (official)

AWS Setup

• OHDSI-In-a-Box
• OHDSI Tools Required
  • White Rabbit / Rabbit in a Hat
  • USAGI
    • With indexes prebuilt (documentation)
  • Data
    • OMOP Vocabulary
    • Raw Synthea Data
    • CDM Synthea Data V1
    • CDM Synthea Data V2
    • Raw Lauren Data (empty, SQL generates data)
    • CDM Lauren Data
• R Studio, R, OHDSI R Packages
  • DB Connector
  • SQL Render