COVID-19 Data Processing Pipelines and datasets

This repository hosts workflows to process several data sources and cleaned datasets for COVID-19 cases across the world.

Datasets

Historical (daily) case data

• owid-covid-data.json: European Centre for Disease Prevention and Control (ECDC) historical world-wide case data (currently through Our World in Data).

• output/cases/cases_us_states_nyt.csv: US state-level historical case data from New York Times.

Country metadata

• World Bank Data: Classification of world region (Latin America & Caribben, South Asia, Sub-Saharan African, Europea & Central Asia, Middle East & North Africa, East Asia & Pacific, North America) for each country or area is based on data_source/metadata/worldbank/country_metadata.csv from World Bank.
• ISO-3166-Countries-with-Regional-Codes: For countries or areas not found in World Bank data, their world region is found in ISO-3166-Countries-with-Regional-Codes.

Historical case data for visualizations

• cntry_stat_owid.json: ECDC historical data merged with Worldbank's classification of world regions. Used in:
  • an interactive visualization of case fatality rate of COVID-19
    • Website source code: covid19-data/covid19-dashboard
    • visualization source code on ObservableHQ: https://observablehq.com/@yy/covid-19-fatality-rate and https://observablehq.com/@yy/covid-19-spreading-trends
  • An example to create case time series charts in ObservableHQ by benjyz
  • You can find the data manipulation process of cntry_stat_owid.json here.
• us_state_nyt.json: New York Time historical data. Used in:
  • New cases vs. all confirmed interactive visualization.

Note

Cases on cruise ships were classified as "international". These data were not shown in the visualizations independently but were included in cases within the data for the "World".

Deprecated

WHO dataset is deprecated. See Our World in Data's announcement: Why we stopped relying on data from the World Health Organization

• output/cases/cases_WHO.csv

• https://www.worldometers.info/coronavirus/

• coordinates.csv: Lat Lng location data from JHU dataset (Unreliable).

• ISO 3166-1 Alpha-3 country code conversion table.

  • output/metadata/country/country_name_code.csv: a conversion table from country name to code (ISO 3166 Alpha 3). Note that multiple names point to the same code.
  • output/metadata/country/country_code_name.csv: a conversion table from country code (ISO 3166 Alpha 3) to country name. The shortest country names are picked from the above dataset.

Usage

Install pandas and snakemake using conda.

conda install -c bioconda -c conda-forge snakemake pandas numpy

or pip:

pip install pandas snakemake numpy