cumulus-library-covid 2.1.0

SQL generation for cumulus covid symptom analysis

Cumulus Library - Covid

A collection of tables for generating bioinformatics data for studying COVID-19 symptoms. Part of the SMART on FHIR Cumulus Project.

For more information, browse the Cumulus Library documentation.

Usage

To install the module, simply run pip install cumulus-library-covid.

This will add a covid_symptom study target to cumulus-library.

See RUNNING.md for more details.

Publications

The following publications leveraged this module:

Moving Biosurveillance Beyond Coded Data: AI for Symptom Detection from Physician Notes Andrew McMurry, Amy R Zipursky, Alon Geva, Karen L Olson, James Jones, Vlad Ignatov, Timothy Miller, Kenneth D Mandl medRxiv 2023.09.24.23295960; doi: https://doi.org/10.1101/2023.09.24.23295960

A computable phenotype for patients with SARS-CoV2 testing that occurred outside the hospital Lijing Wang, Amy Zipursky, Alon Geva, Andrew J. McMurry, Kenneth D. Mandl, Timothy A. Miller JAMIA Open, 2023;, ooad047,doi: https://doi.org/10.1093/jamiaopen/ooad047

The SMART Text2FHIR Pipeline Timothy A. Miller, Andrew J. McMurry, James Jones, Daniel Gottlieb, Kenneth D. Mandl medRxiv 2023.03.21.23287499; doi: https://doi.org/10.1101/2023.03.21.23287499 (Preprint)