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UK Biobank health data keeps ending up on GitHub

biobank.rocher.lc

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Re: UK Biobank health data keeps ending up on GitHub

#11

Post by shellac »

John7878781 wrote: post #3

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

'Anonymisation' schemes are a little like encryption, in that they just get monotonically weaker over time as people work out attacks. But the attacks tend to be much worse. I work in academic open data publishing, and the netflix prize (https://arxiv.org/abs/cs/0610105) hangs over our heads.

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.

Re: UK Biobank health data keeps ending up on GitHub

#14

Post by Cynddl »

tptacek wrote: post #13
John7878781 wrote: post #3

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

One of the most important "con"'s is that without controls, fewer people will allow their data to be included in the data sets.

That's a very important point. The people who opt out first are typically not a random fraction of the population, and this makes it much harder to make any analyses with the resulting datasets: it gets very hard to know if your analyses are representative of the population, or not.

Re: UK Biobank health data keeps ending up on GitHub

#15

Post by tptacek »

Cynddl wrote: post #14
tptacek wrote: post #13

Earlier quoted context omitted.

One of the most important "con"'s is that without controls, fewer people will allow their data to be included in the data sets.

That's a very important point. The people who opt out first are typically not a random fraction of the population, and this makes it much harder to make any analyses with the resulting datasets: it gets very hard to know if your analyses are representative of the population, or not.

This is why it was such a big deal when that researcher at Cleveland State misappropriated UKBB data for a race-science study with Emil Kirkegaard. After he was fired, people on Twitter were all like "this is just suppression of science", but the reality is that what they did, contravening UKBB rules, constituted potentially an existential threat to the whole program.

Re: UK Biobank health data keeps ending up on GitHub

#17

Post by yosame »

michaelt wrote: post #10
John7878781 wrote: post #3

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

It's exceptionally difficult to avoid the data being de-anonymised. 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 conse…

In my experience with health data, the dates are usually offset by a random but constant amount for each person (e.g. id 12345 will have all their dates shifted by +5 weeks) to avoid identification by dates.

Unfortunately the sequence of treatments and locations are usually enough to identify someone, especially if it's a rarer condition.

Re: UK Biobank health data keeps ending up on GitHub

#18

Post by 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.

Re: UK Biobank health data keeps ending up on GitHub

#19

Post by 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...

Re: UK Biobank health data keeps ending up on GitHub

#20

Post by nxobject »

anitil wrote: post #19

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...

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...

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