Introduction

This repository has source codes for reproducing methods and analyses in the following paper:

COHD-COVID: Columbia Open Health Data for COVID-19 Research
    Junghwan Lee, Jae Hyun Kim, Cong Liu, George Hripcsak, Casey Ta, Chunhua Weng
    Preprint

To Export Raw Data from OMOP Database via SQL Server Management Studio (SSML)

1. Update settings in SQL Server Manangement Studio so that Results to Text saves tab-delimited files at Tools > Options > Query Results > SQL Server > Results to Text -Output format: tab delimited -Include column headers in the result set: enabled Then restart SSMS for new settings to take effect
2. Enable SQLCMD mode at Query > SQLCMD Mode
3. Execute the query you wanted to export in /sql_queries directory with updated output path after :OUT command.

To Calculate Concept Count, Concept Co-occurrence, and Symptom Prevalence

analysis.py contain functions to calculate the concept count, concept co-occurrence, and symptom prevalence based on the raw data exported from the database. prevalence_example.ipynb contain examples to use the functions in the package.

Analyses using Concept Count, Concept Co-occurrence, and Symptom Prevalence

analysis.py contain functions to perform various analyses based on the concept count, concept co-occurrence, and symptom prevalence results. analysis_example.ipynb contain examples to use the functions and to perfrom analyses in the paper.