Collection of Covid-19 datasets and analyses

[pchalasani (Prasad Chalasani)]

Over the past couple weeks I’ve been collecting various Covid-19 related datasets. It would be great if there’s a single repository that collects all of these in one place, but I thought I’d share my findings here, with a brief comment/description about each. These are from my personal notes, so please excuse the rough form of these. It could be a starting point to which others can add.

• Comprehensive Covid-19 resources from ESRI/GIS

  • https://coronavirus-resources.esri.com/

• Basic Daily updated Johns Hopkins U data

  • https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data

• Covid-19 - fast.ai forum

  • https://forums.fast.ai/c/covid-19

• Auto-updated Dashboards built using fastpages and updated using github actions, from above JHU data:

  • This is a fantastic set of notebooks that pull the JHU data, so we can re-use some of the pre-processing they do
  • https://covid19dashboards.com/
  • This one is especially interesting: Uses additional country-level covariates to estimate mortality rates:
    • https://covid19dashboards.com/covid-19-mortality-estimation/#Interpretation-of-Country-Level-Parameters

• Help With Covid – call for project proposals and volunteers

  • https://helpwithcovid.com/

• Web-app built from Streamlit

  • https://covid19.cwerner.ai/

• Impressive visualizer of country numbers

  • https://boogheta.github.io/coronavirus-countries/

• Kaggle data (snapshot of JHU data)

  • It has multiple time series data, including age, gender
  • https://www.kaggle.com/sudalairajkumar/novel-corona-virus-2019-dataset

• Another Kaggle dataset:

  • This is the simplest dataset, updated daily: [EDIT; FIXED THIS LINK]
    date, region, lat, long, confirmed, dead, recovered
  • https://www.kaggle.com/imdevskp/corona-virus-report

• “Humanitarian data”, also possibly related to JHU data

  • https://data.humdata.org/dataset/novel-coronavirus-2019-ncov-cases

• Weather + Covid

  • Reddit – [Project] I’ve compiled weather/climate date for the confirmed COVID19 infection sites, if anyone wants it
    https://reddit.com/r/MachineLearning/comments/fh2rr6/project_ive_compiled_weatherclimate_date_for_the/

• Covid19 Tracker (US ONLY!) (https://covidtracking.com/)https://covidtracking.com/

  • date, state, positive, negative, pending, death, total
  • 2020-Mar-04 to now

• Our World In Data Coronavirus Source Data (from WHO)

  • date, country, new_cases, new_dead, tot_cases, tot_dead
  • 2020-Feb-25 to now
  • Nicely formatted version:
    • https://data.world/markmarkoh/coronavirus-data
  • How to pull data from data.world:
    • https://gist.github.com/markmarkoh/7ff3ca8c0a92cc6f8822a6db36f29b68

• Microsoft covid19 tracker (but no raw data)

  • https://www.bing.com/covid

• Call to Action to the Tech Community on New Machine Readable COVID-19 Dataset

  • This is not numerical data, but text data from research articles, and the goal is to answer various questions with NLP

• Covid-19 Chest X-Ray Data

• China data age sex fatality

  • http://weekly.chinacdc.cn/en/article/id/e53946e2-c6c4-41e9-9a9b-fea8db1a8f51
  • Related China paper
    • https://jamanetwork.com/journals/jama/fullarticle/2762130

• Nice simulations

  • https://meltingasphalt.com/interactive/outbreak/

• Singapore covid surprisingly detailed data and dashboard (MIT Tech Review)

  • https://co.vid19.sg/
  • https://www.technologyreview.com/s/615370/coronavirus-pandemic-social-distancing-18-months

• Project notebook showing [[covid19]] detection from chest x-ray images

  • https://www.pyimagesearch.com/2020/03/16/detecting-covid-19-in-x-ray-images-with-keras-tensorflow-and-deep-learning/

• Scale-AI will provide free data-labeling/annotation service for researchers working with [[covid19]] datasets:

  • https://scale.com/blog/scale-ai-covid-19-research

[brunosan (Bruno Sánchez-Andrade Nuño)]

some external resources that might be useful:

Crowdsourcing data:

COVID-19 Global Impact Survey: Awareness

COVID-19 Global Impact Survey: Economics

COVID-19 Open Research Dataset (CORD-19): Access this dataset to help with the fight against COVID-19. In response to the COVID-19 pandemic, the Allen Institute for AI has partnered with leading research groups to prepare and distribute the COVID-19 Open Research Dataset (CORD-19), a free resource of over 29,000 scholarly articles, including over 13,000 with full text, about COVID-19 and the coronavirus family of viruses for use by the global research community. This dataset is intended to mobilize researchers to apply recent advances in natural language processing to generate new insights in support of the fight against this infectious disease. The corpus will be updated weekly as new research is published in peer-reviewed publications and archival services like bioRxiv, medRxiv, and others. https://pages.semanticscholar.org/coronavirus-research

LitCovid: LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus. It is the most comprehensive resource on the subject, providing a central access to 1263 (and growing) relevant articles in PubMed. The articles are updated daily and are further categorized by different research topics and geographic locations for improved access. You can read more at Chen et al. Nature (2020) and download our data here. https://www.ncbi.nlm.nih.gov/research/coronavirus/?utm_source=Nature%20Briefing&utm_campaign=2033dfb840-briefing-dy-20200318&utm_medium=email&utm_term=0_c9dfd39373-2033dfb840-43229289

[pchalasani (Prasad Chalasani)]

Just saw a Korea dataset, which could be good given the extensive testing they’re doing there:

• Korea Dataset:
  • patient level, and also patient movement routes
  • https://github.com/ThisIsIsaac/COVID-19_Korea_Dataset

[tomassa (Tom)]

Terra app for biomedical research released COVID19 Best practice workflows https://support.terra.bio/hc/en-us/articles/360040613432

• I ran few workflows, technically quite easy but need to have biology knowledge to understand semantics
• it runs on top of GCP and Jupyter notebooks, uses Python, R and WDL for workflow definition
• free datasets with anonymized biosamples, sequencing data, sequencing centers and platforms…

[Cartwright]

Thanks for the information. Keep suggesting such post. Looking for the same info.

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