UK Biobank health data keeps ending up on GitHub

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

197 points by Cynddl 25 days ago | 57 comments

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.

michaelt 24 days ago |

> 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 :(

petterroea 24 days ago | |

One of the favorite lessons I learned is that anything at scale has to be designed for idiots. I am pretty sure every person reading this has had days where they have done absolutely stupid things without realizing. Now assume there are thousands of users, and you could be providing tools to the smartest people in the world and still have people do stupid stuff all the time. This doesn't just apply to UX.

Then there's the question of trust. You probably have friends you know not to tell certain secrets to, because they believe they get to delegate your secrets onwards to people they trust. The further away someone is from you, the less respect they will show. Researchers have been loaning the dataset in good faith to people who they trust, but who probably didn't take the whole secrecy thing as seriously.

With 20k researchers this was inevitable. The kind of factors above need to be factored in when designing on what grounds such a dataset is to be released.

LeifCarrotson 23 days ago | | |

"Favorite" in what sense? "Most critical" is a very different meaning of the word, usually it implies pleasure/happiness.

Internalizing that people are frequently less intelligent and less respectful and less kind and less thoughtful than you previously believed is a tragic loss of innocence and hope, not a favorable experience.

hulitu 21 days ago | | |

> One of the favorite lessons I learned is that anything at scale has to be designed for idiots

And in the end it is designed _by_ idiots and only idiots find it usable.

ACCount37 24 days ago | |

Not giving the data to researchers means not getting the scientific benefits from that data. Which was the point of collecting that data in the first place.

Reckless harm prevention is the root of many evils.

nxobject 24 days ago | | |

As a biostatistician who's touched epidemiological studies, I'd argue losing the trust of participants and the public is one of the biggest threats to the viability of the whole research enterprise. It's reckless to jeopardize that as well. Conversely, this dataset will be mined for at least 30-50 years - there are an infinite number of questions that can be asked of this dat. Given that timescale, I think a little delay here is acceptable.

Cynddl 24 days ago | | |

It's not a zero-sum game, you can both protect people and reap the benefits of health data. Many countries have much safer approaches. UK Biobank typically leads with the scale of the data, but not with its infrastructure.

bonesss 24 days ago | | |

That’s a false dichotomy.

Sensitive research systems thread that needle by giving remote access to researchers with the data in the control and supervision of the responsible organization. Strong internal data access controls and data siloing alongside strict verified extraction routines. Specifically: limited project-dedicated DB access, full logging of data interactions, and full lockouts/freezes if something feels off.

‘The five safes’ is a good presentation from the NHS(?) a decade ago covering the approaches.

Data publishing restrictions around health data aren’t reckless. Modern computing and digital permanence mean we have to be extra cautious.

SilverElfin 24 days ago | |

That’s insane. And what does researcher even mean - some random university student? What would they know about securing that data? I wonder if the people whose data is out there even know this is happening

7bees 24 days ago | | |

The people involved are volunteers. The rules for getting access are readily available, and clearly don't include "some random university student": https://www.ukbiobank.ac.uk/about-us/how-we-work/access-to-u...

adwf 24 days ago |

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...

nxobject 23 days ago | |

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."

fastaguy88 24 days ago | |

BioBank claims (1) only de-identified data was available and (2) none of the data was actually sold before the datasets were taken down.

john_strinlai 24 days ago | | |

unfortunately for most people, de-identified data is typically a very short analysis away from being re-identified.

the field of de-anonymization is booming.

anitil 24 days ago |

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...

mfld 24 days ago | |

This is the right mindset. Securing huge piles of heterogeneous data while giving PhD students the freedom to "play" with it are quite conflicting goals.

nxobject 24 days ago | |

I like their idea of an audit log of analysis runs -- beyond transparency, I'm sure it'll help future researchers know how much iteration is needed to work with the messiness of medical records...

I'm also amused (in a good way) by the fact that SAS isn't supported as an analysis platform...

anitil 24 days ago | | |

It's certainly an interesting idea, I remember he was on a few podcasts talking about it. I might submit it here to see if it gets some conversation going

philipwhiuk 24 days ago | |

I have huge problems with Goldacre's project because that project has never been disclosed to the general public let alone some form of opt-in/opt-out.

harvey9 24 days ago | | |

I think the opt out process is the same as the one that came to prominence in the care.data days. It is not a very good process since it is opt out not opt in, and reliant on motivated people searching for a form.

On the other hand I like opensafely's approach to security: no individual data is ever shared with researchers.

captn3m0 24 days ago |

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

Cynddl 24 days ago | |

Good catch! The data is everywhere, re-uploaded every week.

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.

philipwhiuk 24 days ago | |

I don't think either of those links contain actual PII (or anonymised PII).

(The first is a GitHub repo for https://www.weizmann.ac.il/math/tanay/home )

mil22 24 days ago |

The irony is, they don’t even provide the data to the participants themselves.

vain 24 days ago | |

Huh? I got my report over email. I think you have to ask for it.

nxobject 24 days ago |

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.

John7878781 24 days ago |

What are the pros/cons of just open-sourcing everything for future bio bank projects?

dariosalvi78 24 days ago |

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.

paulwetzel 24 days ago | |

I cant really understand why Jupyter Notebooks do this in the first place. It makes it (a) really hard to version control, as there will always be some random blob of non-textual data in the notebook that pops up in a diff and makes it basically unreadable and (b) I can't really see the benefit, as it only stores some part of the data, and not the full table, as far as I am aware.

Enforcing Jupytext is a good adaption, and gives you all the, arguably really nice, comfort from a notebook, and the proper code practice from SW engineering.

lmc 24 days ago | |

marimo notebooks give you the best of both worlds (https://marimo.io)

NGRhodes 24 days ago |

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).

anordal 24 days ago |

Have medical researchers not heard of gitignore? Any hypothesis about the mechanism here?

khelavastr 23 days ago |

UK government fails to prosecute criminally negligent software developers..

mhh__ 24 days ago |

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?

deknos 24 days ago |

so.. where can i get this data? XD