> 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.
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.
> 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.
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 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.
'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.
The people who agreed to contribute their biodata did not consent to that.
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
You mean giving anyone access to the data? Or open sourcing the code? If the latter, I think that's a generally a good practice. Security through obscurity is never good for public infrastructure. In this case, UK Biobank has now switched to a remote access platform (not particularly secure, as the data was found for sale on Alibaba today), but contracting it to DNAnexus and Amazon. Private companies have no incentives to open source data, unless mandated to do so.
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.
Hard to do. The same people with the collection and tracking infrastructure required are infinitely sue-able so you need legal protection if anything goes wrong.
The irony is, they don’t even provide the data to the participants themselves.
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
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.
> 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 :(
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 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.
'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.
The people who agreed to contribute their biodata did not consent to that.
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
You mean giving anyone access to the data? Or open sourcing the code? If the latter, I think that's a generally a good practice. Security through obscurity is never good for public infrastructure. In this case, UK Biobank has now switched to a remote access platform (not particularly secure, as the data was found for sale on Alibaba today), but contracting it to DNAnexus and Amazon. Private companies have no incentives to open source data, unless mandated to do so.
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.
Hard to do. The same people with the collection and tracking infrastructure required are infinitely sue-able so you need legal protection if anything goes wrong.