Monitoring COVID-19 effects

As global trade and economics, indeed, the fabric of society is twisted up in these very troubled times, open data cooperation can be a lightpost for collective action, and a way to help keep each other afloat. Though sometimes, it is the little things that count. A helpful sign on the door, a mood lifting note, a mask, an improved form.

Some of us here are being drawn to question and monitor the decisions of governments and other institutions. Others are called in to assist in restoring trust in a time of great information discrepancy, and ensuring that critically needed measures are being followed. Any of us that can provide valuable support to the medical and health research community are hopefully able to do their very best.

Since the epidemic escalated and lockdown measures were enforced, a rapidly organized collective of about 40 of us in the local open data scene rallied together with a handful of public health experts and supportive government workers to prepare and improve datasets of national cases counts, health infrastructure capacity, monitoring environmental impact and control measures in an online workshop. We’ve been at it day and night all in hope to make a dent in the right direction.

Our efforts are organized on, as much as possible open source, self-hosted platforms like Dribdat, CodiMD, Mattermost, Jitsi Meet and Discourse. We are starting to push results to GitHub and open data portals. 2 days remain in our sprint if you would like to contribute.

There are a number of even smaller and much bigger efforts happening around the world. Looking forward to hearing about yours! Let me know if I can help you get started. Stay tuned for ways our wider community is being engaged in the days ahead.

It is really difficult for me to write this, knowing how many families being torn apart at the moment, how much suffering and shortage is out there, what a historic test this is to our systems and fundamental institutions. Thank you to everyone here, not losing time or resolve, and watching out for one another.

Winston Churchill may have once said “Never let a good crisis go to waste”, and if there is a silver lining to this deadly cloud, it is that the purposes and practices of open knowledge are key to winning battles in the raging infodemic of misinformation.

The other thing they say the man had said is “If you’re going through hell, keep going.” Thank you Catherine & team for encouraging us to keep chins up and stay open.

I sincerely wish all of you the strength and courage to stay strong and do the right thing. Don’t just grit and bear it. Share your story!


Two similar coronavirus data projects.

German coronavirus hackathon

  • 22–25 March 2020
  • strictly open source
  • working language German
  • for 48 hours 42 000 hackers, 27 000 of whom were active, brainstormed over 1500 projects
  • voting finishes on Thursday 26 March 2020.

More background:

Most projects involve social coordination in various settings to maximize social distance, reduce delays, or assist the elderly and immune‑compromised, using websites and apps of course. But some are more complex, involving medical resource allocation, analysis of anonymized social data, and medical imaging interpretation for use in less sophisticated health care environments.

Knowledge graph project

There is a community effort to build a Neo4j Knowledge Graph (KG) that links heterogeneous data about COVID‑19.

Infectious disease propagation modeling

Data and modeling are usually difficult to separate. This posting focuses on code.

UK pandemic researcher Neil Ferguson was discussing his infectious disease propagation codebase on twitter on 22 March 2020:

Analysis of this kind is one of several inputs and considerations the United Kingdom government uses to formulate its evolving public policy response to the coronavirus pandemic.

I gimped an early part of twitter thread, pulling out some of the more interesting comments. What had evidently occurred is an indictment on much of modern science: opaque, unreproducible, and lacking adequate quality control. Microsoft and GitHub are now refactoring and developing the codebase under open source development methods.

Here is an overview of our sprint and projects:

We just announced a nation-wide event on the footsteps of #WirVersusVirus:

Comments and tips on how to keep focused on meaningful results welcome!

This is one of the largest collection of open data efforts on COVID-19, as far as I know (at least among those I’ve seen used in the Italian community):

There’s also a community on Zenodo where I’d encourage anyone to post and mirror code and data, whether theirs or others’:

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I’d like to point your attention to the “control measures” tracking has been one of the loudest discussion points in our event last week. At the international level, we might want to support and extend or even groundswell this kind of effort:

On open science see also:

For countless other efforts in the information space, see:

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The Heinsberg study in Heinsberg, Germany, near the Dutch border, is already producing interesting results:

Around 40 volunteers have been scraping official reports from the state Health Secretariats in order to obtain daily, city-level data on Covid-19 in Brazil. The data is then made available as open data, as bulk CSV downloads, as an API as well as a web form.

The Brazilian chapter of Open Knowledge has also been evaluating the transparency of Brazilian states in regards to the disclosure of Covid-19 data.

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StackExchange thread that might be of interest:

This has been an eye opener. My nephew introduced me to geometric progression while explaining the spread of flu. The Covid-19 lock down has got me thinking of things I otherwise would never think about.

We’ve been following an intense campaign on the side of the authorities and civil society around contact tracing in Switzerland. These explanatory materials might be of interest/use to others, especially if your country is also deploying DP-3T.