COVID-19 dataset clearinghouse

This is a repository for public data sets relating to the COVID-19 pandemic. It was also initially envisioned as a clearinghouse for matching requests for data cleaning of such datasets with volunteers willing to perform this clearing, but the existing clearinghouse at Data against COVID is already up and running for this purpose, so we are redirecting such requests to that site in order not to fragment the pools of requests and volunteers.

For discussion of this project, see this blog post.

Data sets

Epidemiology

• Novel Corona Virus 2019 Dataset - Day level information on covid-19 affected cases, Kaggle
• Coronavirus Disease (COVID-19) – Statistics and Research, Our World in Data, by Max Roser, Hannah Ritchie and Esteban Ortiz-Ospina
• Novel Coronavirus (COVID-19) Cases, Johns Hopkins University Center for Systems Science and Engineering
  • Novel Coronavirus 2019 time series data on cases, sourced and cleaned from the above data set
• 2019-nCoV Data Processing Pipelines and datasets
  • Countries and state names are normalized with ISO 3166-1 code.
• Location for summaries and analysis of data related to n-CoV 2019, first reported in Wuhan, China, Outbreak and Pandemic Preparedness team at the Institute for Health Metrics and Evaluation, University of Washington
  • A visualization of one of the data sets
• Daily data on the geographic distribution of COVID-19 cases worldwide, European Centre for Disease Prevention and Control
• Google sheets from DXY.cn
  • Contains some patient information [age,gender,etc]

North America

• COVID Tracking Data, from the COVID tracking project
  • A daily updated repository with CSV representations of data from the Covid Tracking API.
• COVID-19 in US and Canada
  • Data request form
• COVID tracking project
  • Includes positive and negative results, pending tests, and total people tested for each state in the US
  • raw data
  • API
• Covid-19 coronovirus cases in New York State
• Coronavirus Case Data for Every U.S. County, New York Times

Europe

• Studying SARS-CoV-2 in European patients, Lean European Open Survey on SARS-CoV-2 Infected Patients (LEOSS)
• COVID-19 Italia - Monitoraggio situazione
• RKI COVID19 (Germany), NPGEO Corona
• New coronavirus: Current situation – Switzerland and international, Bundesamt für Gesundheit.
  • data set

Other regional data

• India COVID-19 tracker
  • Patient database
• Data Science for COVID-19 in South Korea
  • The data set on Kaggle
• Latest updates on COVID-19, New South Wales

Genomics and homology

• GISAID data (Global Initiative on Sharing All Influenza Data)
  • Registration is required.
  • Nextstrain build for novel coronavirus (nCoV), based on GISAID data
    • A Genomic epidemiology of novel coronavirus
• Coronavirus Genome Sequence, Kaggle
• Repository of Coronavirus Genomes, Kaggle
• Wuhan coronavirus 2019-nCoV protease homology model, National Institutes of Health

Literature

• LitCovid - a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus
• COVID-19 SARS-CoV-2 preprints from medRxiv and bioRxiv

Medical imagery

• COVID-19 Detection X-Ray Dataset, Kaggle
• COVID-19: casistica radiologica Italiana, Società Italiana di Radiologia Medica e Interventistica

Other data

• Aggregated foot traffic data, Safegraph
  • Needs non-commercial agreement to execute.
  • Sample visualization of Safegraph data
• COVID Care Map
  • Open geospatial work to support health systems' capacity (providers, supplies, ventilators, beds, meds) to effectively care for rapidly growing COVID19 patient needs
  • Open map data on US health system capacity to care for COVID-19 patients
• Covid-19 Twitter chatter dataset for scientific use, Panacea Lab, Georgia State University

Data scrapers and aggregators

• Corona Data Scraper
• Covid19-WebScrape-Plus
• COVID-19, Seektable

Visualizations and summaries

• COVID-19 Coronavirus Pandemic, Worldometer
• Tracking coronavirus: Map, data and timeline, BNO News
• Coronavirus COVID-19 Global Cases, JHU CSSE
• Infection2020
• covy.app
• COVID-19 Global Pandemic Real-Time report, dxy.cn (English version)
• Coronavirus tracked: the latest figures as the pandemic spreads, Financial Times
• COVID-19 - official Indian government site
• COVID-19 - Analysis, Visualization & Comparisons, Kaggle

Other lists

• COVID-19 data sets, Kaggle
• Reddit thread collecting coronavirus datasets
• Review of COVID-19 APIs, Wendell Santos
• Data against COVID-19

Data or Data cleaning requests

As mentioned at the top of this page, future requests for data or data cleaning should be directed to Data against COVID. Below are the legacy requests of this project prior to this redirect.

From Chris Strohmeier (UCLA), Mar 25

The biorxiv_medrxiv file at https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge contains another folder titled biorxiv_medrxiv, which in turn contains hundreds of json files. Each file corresponds to a research article, at least tangentially related to COVID-19.

We are requesting:

• A tf-idf matrix associated to the subset of the above collection which contain full-text articles (some appear to only have abstracts).
• The rows should correspond to the (e.g. 5000) most commonly used words.
• The columns should correspond to each individual json file.
• The clean data should be stored as a npy or mat file (or both).
• Finally, there should be a csv or text document (or both) explaining the meaning of the individual rows and columns of the matrix (what words do the rows correspond to? What file does each column correspond to).

Contact: c.strohmeier@math.ucla.edu

From Juan José Piñero de Armas (U. Católica de Murcia), Mar 27

We request information (on a person basis) to perform survival analyses, regressions with random effects, etc. Some data exists for instance at

https://www.kaggle.com/sudalairajkumar/novel-corona-virus-2019-dataset/data https://www.kaggle.com/kimjihoo/coronavirusdataset https://www.kaggle.com/imdevskp/covid-19-analysis-visualization-comparisons/data https://www.sirm.org/category/senza-categoria/covid-19/

but we need much more detail (date when each person was diagnosed, date of infection for the same person, discharge date, date of death, gender, age, treatments, temperatures...) not just summaries or country-aggregated data.

Contact: jjpinero@ucam.edu