NUHDSS-Residence-VA-ETL-to-OMOP

This repository describes the ETL process for Nairobi Urban HDSS ETL to OMOP and how to visualize in ATLAS

It contains code, and information to extract, transform and load ALPHA source data from Nairobi Urban HDSS (NUHDSS) to a local instance OMOP database.

Software needed

• White rabbit
• Rabbit in a hat
• Usagi
• DBMS(Postgres, MySQL, SQLite etc)
• R

STEPS FOLLOWED

1. Data cleaning and Exploratory data analysis.

2. Data Profiling and Mapping.

3. Vocabulary Mapping.

4. ETL Implementation. I used PostgreSQL to write SQL scripts for transforming source codes to OMOP terminologies. Penataho can equally be used for ETL Data Quality Assurance: OHDSI library for quality assurance of the CDM 'DataQualityDashboard' was installed and run against the OMOP database. Visit OHDSI DQD GitHub for more information on DQD documentation and installation.

5. Data Quality Checks to generate DQD Dashboard.

6. Generating Aggregated (Results tables) data for Atlas using Achilles R library by OHDSI for data characterization tool. This is an automated process using codes developed by OHDSI

7. Visualization in Atlas : Aggregated data(results tables), OMOP tables and vocabulary tables were integrated with Atlas and webAPI

Visit OHDSI GitHub for more information.