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The exposure of Biobank data on GitHub is the latest in a long series of governance challenges for UK Biobank. (My colleague and I have an editorial in the BMJ about this: http://bmj.com/cgi/content/full/bmj.s660?ijkey=dEot4dJZGZGXe...). The latest is today, with information of all half a million members listed for sale on Alibaba.
Looking at the takedown notices, we often see specific files being targeted rather than entire repositories (possibly to justify the copyright infringement as required for a takedown notice, not a copyright expert; although it is clear that they only use DMCA notices as a last resort, for GitHub users they cannot identify, and who were likely not given access in the first place). A quarter of the files are genetic/genomics. Tabular data account for another large share and could contain phenotype or health records.
Discussion (12 Comments)Read Original on HackerNews
To me it seems rather naive to have done that.
After all, you can't un-leak medical data. So even if the "strict agreement" included huge punishments, there's no getting the toothpaste back in the tube.
If you want to ensure compliance before a leak happens you have to (ugh) audit their compliance. And that isn't something that scales to 20,000 researchers.
Too late to do anything about it now though :(
And some information on how they were distributing it to researchers: https://github.com/broadinstitute/ml4h/blob/master/ingest/uk...
> The following steps require the ukbunpack and ukbconv utilities from the UK Biobank website. The file decrypt_all.sh will run through the following steps on one of the on-prem servers.
> Once the data is downloaded, it needs to be "ukbunpacked" which decrypts it, and then converts it to a file format of choice. Both ukbunpack and ukbconv are available from the UK Biobank's website. The decryption has to happen on a linux system if you download the linux tools, e.g. the Broad's on-prem servers. Note that you need plenty of space to decrypt/unpack, and the programs may fail silently if disk space runs out during the middle.
https://biobank.ctsu.ox.ac.uk/crystal/download.cgi
I am aware of ~30 repositories that UK Biobank has asked GitHub to delete, and can still be found elsewhere online. They know the site, they have managed to delete data from that site before, and yet the files are still there.
If an 'anonymised' medical record says the person was born 6th September 1969, received treatment for a broken arm on 1 April 2004, and received a course of treatment in 2009 after catching the clap on holiday in Thailand - that's enough bits of information to uniquely identify me.
And medical researchers are usually very big on 'fully informed consent' so they can't gloss over that reality, hide it in fine print or obsfucate it with flowerly language. They usually have to make sure the participants really understand what they're agreeing to.
It might still work out fine, of course - 95% of people's medical histories don't contain anything particularly embarrassing, so you might be able to get plenty of participants anyway.
But what this illustrates to me is that researchers are just really careless, despite everything we make them agree to in data transfer agreements. It seems absurd to have little cubicles like this https://safepodnetwork.ac.uk/ (think Mission Impossible 1) but I do despair.
In the EU, there is a bigger interest in building scalable but also secure platforms for health data. Hopefully good innovation will come from there.
If you want such a project you need to have a new project with a different agreement. I doubt you could get as many volunteers to freely give away such intimate data to anyone who wants though