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 United against COVID-19 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

Further contributions are very welcome, and can be made either directly to this wiki page (after requesting an account), or placed in the comments to this blog post, or by email to tao@math.ucla.edu.

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
  • Cases + mortality rate daily
• 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]
• COVID-19 Complete Dataset (Updated every 24hrs), Kaggle
• Epidemic Data for Novel Coronavirus COVID-19, Wolfram
• Coronavirus COVID-19 Cases, ESRI

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 USA, Kaggle
• COVID-19 Cases US, ESRI
• 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
• Sorveglianza integrata COVID-19: i principali dati nazionali (Italy), Epicentro
• COVID-19 in Italy, Kaggle
• RKI COVID19 (Germany), NPGEO Corona
• New coronavirus: Current situation – Switzerland and international, Bundesamt für Gesundheit.
  • data set
• Situacion Actual (Spain), Ministerio de Sanidad, Consumo y Bienestar

Asia

• India COVID-19 tracker
  • Patient database
• Dataset on Novel Corona Virus Disease 2019 in India, Kaggle
• COVID-19 Corona Virus India Dataset, Kaggle
  • State/UT/NCR wise COVID-19 data
• Data Science for COVID-19 in South Korea
  • The data set on Kaggle
• Press releases, Korea Centers for Disease Control and Prevention

Other regional data

• Coronavirus (COVID-19) - Brazil Dataset, 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
• SARS coronavirus accession, Kaggle
  • Exploration of mutations of the SARS corona virus with complete genome
• Genetic Sequences for the SARS-CoV-2 Coronavirus, Wolfram
  • Nucleotide sequences of the SARS-CoV-2 virus (the virus associated with the COVID-19 disease, formerly known as 2019-nCoV) including location, collection time and similar supporting data.
• 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
• COVID-19 Open Research Dataset (CORD-19), Allen Institute for AI, Microsoft, NLM, CZI, Georgetown University
  • Over 44,000 scholarly articles, including over 29,000 with full text, about COVID-19 and the coronavirus family of viruses for use by the global research community
  • requested by the White House Office of Science and Technology Policy, and part of the Call to Action to the Tech Community on New Machine Readable COVID-19 Dataset

Medical imagery and records

• Patient Medical Data for Novel Coronavirus COVID-19, Wolfram
• COVID-19 Detection X-Ray Dataset, Kaggle
• COVID-19: casistica radiologica Italiana, Società Italiana di Radiologia Medica e Interventistica

Healthcare

• Definitive Healthcare: USA Hospital Beds, ESRI
• COVID-19 Provider Practice Locations, ArcGIS.

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
• COVID Act Now - predictions of COVID cases in the US by state
  • The model used
• An interactive visualization of the exponential spread of COVID-19

Other lists and groups

• COVID-19 data sets, Kaggle
• Reddit thread collecting coronavirus datasets
• Review of COVID-19 APIs, Wendell Santos
• NPGEO Corona Hub 2020, Nationale Plattform für geografische Daten (NPGEO)
• Data sets for COVID, Wolfram Data Repository
• COVID-19 Data Hub, Tableau
• COVID-19 GIS Hub, ESRI
• Coronavirus (COVID-19) Data, ESRI
  • This is a collection of data that is available from the Esri Living Atlas as well as data from authoritative sources.

Data or Data cleaning requests

As mentioned at the top of this page, future requests for data or data cleaning should be directed to this data discourse page at United Against COVID-19. 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