Here is a synthetic omop csv data set that contains a covid pandemic. I started with synthea covid branch and generated a dataset for MA, USA. This was converted to omop using ETL-Synthea project. The pandemic starts Jan1.2020 and affects all 10K patients on a standard distribution over a period of 3 months.
Let me know if any particular need for synthetic data. I am building azure pipelines to generate it on a schedule.
Does this include more specific COVID-19 diagnoses and tests coded with appropriate SNOMED, ICD-10 and LOINC codes? What about SARS-CoV-2 positive patients with other manifestations (pneumonia, ARDS, etc.) that require multiple ICD-10 and/or SNOMED codes per diagnosis? Thanks!
It contains specific COVID-19 diagnosis and tests coded with SNOMED and LOINC. Synthea does not use ICD10 as it requires payment.
Survivor, non survivor lab values based on Figure 2 from https://doi.org/10.1016/S0140-6736(20)30566-3
“Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study”
Here are some examples:
49727002, Cough (finding)
386661006, Fever (finding)
267036007, Dyspnea (finding)
Michael, are you still creating COVID synthetic data? We’re standing up our OHDSI infrastructure on Azure, and want to start testing the environment, and sizing our needs, based upon a population size of about 2 million patients.
Generate data with synthea (at the time there was a covid branch and they have made a lot of improvements since then. Not sure if they merged that one)
Convert data with ETL-Synthea.
I didn’t get ETL-Synthea to scale over around 50k patients. The scripts would fail in postgres even with my laptop having 32GB of ram and ssd drive. They try to process the data all at once and not in batches.