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Is there anywhere a database that includes case-level information on COVID-19 cases?

Such data would typically include patient demographics and/or health information, location, time of onset/testing, and case outcomes.

Even data from one (or several) specific locations would be most helpful.

This question refers to case-level data. For aggregate data, see this question (COVID19 - Corona Virus data).

philshem
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dzeltzer
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    Given the sensitivity of such PII and PHI under HIPAA and other patient/respondent privacy laws, it is unlikely to be available at case-level. If it ever does, it will more than likely be masked to some degree. – Kotebiya Mar 18 '20 at 13:47
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    Also looking for such data. I‘m interested in looking at mortality contingent on demographics and individual patient information. – Peter Mar 20 '20 at 21:17
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    @Kotebiya sure, but even masked data (coarsened age, location, etc.) could be useful. – dzeltzer Mar 24 '20 at 15:30
  • Postman (HTTP request & API testing tool) have and still are compiling a list of data sources requestable programmatically:

    https://covid-19-apis.postman.com/ not sure if it's enough for a proper answer in this site, though. You need to filter this, because there are not only clinical data but also "related" API, for instance the correct API endpoints to get the Twitter feed from WHO.

     – Pac0 Jun 19 '20 at 10:26

4 Answers4

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The Anthem XPRIZE Pandemic Alliance has pledged the availability of such de-identified data including data on previous outbreaks (i.e. swine-flu, influenza, SARS etc.) It is unclear, however, how soon the datasets will be released to researchers as it was just announced.

Praxiteles
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I've also found a fairly detailed dataset on github

https://github.com/beoutbreakprepared/nCoV2019/tree/master/latest_data

This is quite exciting as it holds the following data

  • Demography: age,sex
  • Geographic: city, province, country, wuhan(0)_not_wuhan(1), latitude, longitude, geo_resolution, lives_in_Wuhan, location, country_new
  • Dates: date_onset_symptoms, date_admission_hospital, date_confirmation, date_death_or_discharge, travel_history_dates
  • Symptoms: symptoms
  • Other disease: chronic_disease_binary, chronic_disease
  • Exposure: travel_history_location, reported_market_exposure, travel_history_binary
  • Outcome: outcome,
  • Other: additional_information, source, sequence_available, notes_for_discussion, admin3, admin2, admin1, admin_id, data_moderator_initials

The downside, is that the data is of mixed quality, but it is critiqued by medical and data specialists. Some fields are completely left blank, but as a research source it could be a great place to start.

(This answer was moved from a more general question)

Marcus D
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  • Fwiw, countries with hospitalization dates for > 100 patients, with last date (latestdata.csv from August 28): Argentina 7267 2020-06-08, China 1161 2020-03-05, Cuba 234 2020-04-29, France 100063 2020-06-03, Japan 124 2020-02-28, Netherlands 6731 2020-05-11, Singapore 280 2020-03-09 – denis Aug 30 '20 at 13:11
  • Interesting. So probably dependent upon hospitals in particular countries submitting data. Thx – Marcus D Sep 02 '20 at 09:54
  • does anyone know offhand which of these (at the end, below) have data up to August ? And which come with csv sanity checkers ? – denis Sep 02 '20 at 10:28
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South Korea has opened patient data. From what I glean from these tweets:

https://twitter.com/sang_woo_park/status/1247222889222483969

South Korea released medical history for all #COVID19 patients based on their insurance claims for the past five year:

https://hira-covid19.net/

https://twitter.com/sang_woo_park/status/1247386655549526017

The website is a bit cryptic. The sample data can be found in the "notice" menu under the "community" tab after logging in, but the data schema is in Korean. If you're serious about analyzing the data, I might be able to help with the translation...

https://twitter.com/FabiKrauer/status/1247467016006651905

„Raw data will not be available for download nor transmission. Researchers will use the sample data on the website (https://covid19data.hira.or.kr) to produce an analysis code and submit the code to HIRA through this website. In return, HIRA will deliver the analysis result values“

PDF user manual: https://rtrod-assets.s3.ap-northeast-2.amazonaws.com/static/tools/manual/COVID-19+website+manual_v2.1.pdf

It requires registration, and I think you have to do the analysis inside the platform.

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philshem
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Would like to add few more resources

There is a large body of research and data around COVID-19. Help the global community better understand the disease by getting involved on Kaggle.

Datasets in Kaggle related to COVID

Popular datasets

WHO Coronavirus Disease (COVID-19)

" The EULAR - COVID-19 Database is a European pediatric and adult database (in collaboration with the Pediatric Rheumatology European Society (PReS)) to monitor and report on outcomes of “Coronavirus Disease 2019” (COVID-19) occurring in patients with rheumatic and musculoskeletal diseases (RMDs). "

Ref.: The COVID-19 Global Rheumatology Alliance. Website

Please visit: The European League Against Rheumatism (EULAR)

Here is a list of open-source databases for COVID-19 case reports,

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  • Does anyone know offhand which of these have data up to August ? And which come with csv sanity checkers ? Thanks – denis Aug 30 '20 at 13:13