HN Explorer

UK Biobank health data keeps ending up on GitHub (biobank.rocher.lc)

197 points by Cynddl ↗ HN
I'm a researcher studying privacy, and I started tracking the DMCA notices that UK Biobank sends to GitHub. I tracked 110 notices filed so far, targeting 197 code repositories by 170 developers across the world.

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.

18 comments

[ 739 ms ] story [ 157 ms ] thread
michaelt
> It has given 20,000 researchers around the world access under strict agreements that prohibit sharing data further.

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 :(

John7878781
What are the pros/cons of just open-sourcing everything for future bio bank projects?
captn3m0
Took me 5 minutes to find more: https://github.com/tanaylab/Mendelson_et_al_2023/blob/9c5a65... (Uses Date of Birth column).

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

mil22
The irony is, they don’t even provide the data to the participants themselves.
adwf
That's the least of it: https://www.bbc.co.uk/news/articles/cpvxgl3n138o

All 500,000 participants for sale on Alibaba...

And official response: https://www.ukbiobank.ac.uk/news/a-message-to-our-participan...

fastaguy88
BioBank claims (1) only de-identified data was available and (2) none of the data was actually sold before the datasets were taken down.
nxobject
More details on leaked information from El Reg, especially after (laudably) the British government has been more transparent: https://www.theregister.com/2026/04/23/500k_biobank_voluntee...

"The charity did not specify the types of data that were included, but Murray stated in the Commons that several markers were included in the listings:

- Gender

- Age

- Month and year of birth

- Assessment center data

- Attendance dates

- Socioeconomic status

- Lifestyle habits

- Measures from biological samples related to haematology, biology, and chemistry

- Sleep, diet, work environment, mental health, and health outcomes data."

nxobject
From the perspective of someone who's worked with (biostatisticians who touch) Medicaid and Medicare billing data...

It looks like they've identified the institutions, at least... but aren't identifying it to the public for now. Are there going to be consequences? Are they going to be identified and sanctioned beyond "having their access suspended?"

In the US, HHS wouldn't hestitate to name, shame, and impose a sanction with corrective action plans. Not knowing much about how things work across the pond, I'm sure CMS PII gets used more often in research without these leaks left and right.

anitil
I've opted in to Australia's version of the biobank knowing that it's inevitable that it will be leaked some day, I think the data is so valuable in perpetuity that it's worth it. I remember Ben Goldacre has been working on how to make data more accessible in a safer way to (in part) avoid this very thing, but I haven't heard much of it since [0]

[0] https://www.bennett.ox.ac.uk/blog/2025/02/opensafely-in-brie...

dariosalvi78
the issue is with jupyter notebooks because they keep some of the data in the output (typically a few rows, but still). They should strongly recommend to use regular python scripts, and keep the jupyter books just for verification, which is a very sane thing to do also from a SW engineering perspective.
deknos
so.. where can i get this data? XD
NGRhodes
Thank you for sharing. I work in a central RSE team and have raised this topic to the team, with a view of bringing attention to this issue and better educating our researchers (as part of our training offerings and documentation).
mhh__
I haven't been paying attention to it but wasn't there some kerfuffle over some people threatening to leak it over not being allowed to publish controversial findings?
anordal
Have medical researchers not heard of gitignore? Any hypothesis about the mechanism here?
khelavastr
UK government fails to prosecute criminally negligent software developers..