4 ms·

>And ? What's not to get? OP said: >... I strongly believe there is enough information to re-identify patients. Their concern is that just dumping raw data l

>And ? What's not to get? OP said: >... I strongly believe there is enough information to re-identify patients. Their concern is that just dumping raw data like this into the public would be a massive violation of privacy for countless individuals.

rvnx 5y ago
Re-identify based on what ? There are no databases that you can link against if you strip out the major identifiers (like city and date of birth). It's for the benefit of patients, and this raw data is already available, but under a loose NDA for commercial partners and researchers...
- throwawaygh 5y ago
  > Re-identify based on what ? The fact that you poo-poo this question is telling. Preventing re-identification attacks is incredibly subtle and sometimes impossible. Removing "city and date of birth" is nowhere near sufficient. > this raw data is already available, but under a loose NDA for commercial partners and researchers... Yes. It's available to people who have their real identities tied to their access and can be sued into oblivion or possibly even prosecuted for wanton misuse of the data. Surely you see how this is different from throwing it on a public s3 bucket, right?
  - rvnx 5y ago
    It looks like from what you are saying that it's an incommensurable effort to anonymize reasonably the dataset (the majority of the risks can be hedge by bucketing, and then there can be subtle deanonymization edge cases but they don't scale). It reminds me the FDA saying they can't release the COVID-19 documents because reviewing 44'000 documents would take 50 years. It didn't take 50 years to produce them... Yes there is some effort needed to anonymize reasonably the data but it's not an impossible task. It's a question of motivation. Here, clearly, the labs and administration don't really want to put efforts into that.
    - throwawaygh 5y ago
      Presumable FDAs analysis assumed current staffing levels. Going to go out on a limb and assume they’ve got a LOT more people involved in creating docs than in deidentifying docs. And, yes, I think public data on this sort of stuff is important and should be properly resourced. I think: Step 1. ASK PERMISSION before changing the way data is handled. Step 2. Share full datasets more generously, but still gated by use and handling agreements. This probably means a private citizens without ethics research training and a supporting it dept can’t get a copy and peruse it on their personal laptop, but also that a truly enormous number of researchers would be able to access the data. The gold standard of a CSV in a public s3 bucket shouldn’t be the enemy of good enough.
- jjulius 5y ago
  I'm not so sure that you should be so sure that there are no databases that such data can be referenced against. Regarding stripping out major identifiers, please note that OP commented that "it's not as simple as just removing the sensitive medical data because the primary or secondary analyses may be dependent on them". And of course raw data like this could benefit patients, but keeping access to raw data limited also benefits patients. Sure, the data is readily available under a loose NDA, but it's available to people who have explicit knowledge of the requirements around handling sensitive, identifiable data. Average Joe's and Jane's do not have this knowledge, and bad actors just plain don't give a shit.
- ashtonkem 5y ago
  I mean, it’s not like anonymous datasets haven’t been de-anonymized before[0]. Successfully anonymizing data sets is a hard and subtle process, and it’s way harder than just removing major identifiers like city and birth date. For example age is obviously super important for vaccine and disease studies, and providing an age narrows down someone’s birthdate significantly. And no, this isn’t under a “loose” NDA. This would be covered by HIPAA, which tends to be un-subtle about violations. 0 - https://www.cs.princeton.edu/~arvindn/publications/de-anonymization-retrospective.pdf https://www.cs.princeton.edu/~arvindn/publications/de-anonym...
- hcknwscommenter 5y ago
  "There are no databases that you can link against if you strip out the major identifiers" Isn't that provably untrue? https://bits.blogs.nytimes.com/2015/01/29/with-a-few-bits-of-data-researchers-identify-anonymous-people/ https://bits.blogs.nytimes.com/2015/01/29/with-a-few-bits-of...

rvnx 5y ago

Re-identify based on what ? There are no databases that you can link against if you strip out the major identifiers (like city and date of birth). It's for the benefit of patients, and this raw data is already available, but under a loose NDA for commercial partners and researchers...

throwawaygh 5y ago
> Re-identify based on what ? The fact that you poo-poo this question is telling. Preventing re-identification attacks is incredibly subtle and sometimes impossible. Removing "city and date of birth" is nowhere near sufficient. > this raw data is already available, but under a loose NDA for commercial partners and researchers... Yes. It's available to people who have their real identities tied to their access and can be sued into oblivion or possibly even prosecuted for wanton misuse of the data. Surely you see how this is different from throwing it on a public s3 bucket, right?
- rvnx 5y ago
  It looks like from what you are saying that it's an incommensurable effort to anonymize reasonably the dataset (the majority of the risks can be hedge by bucketing, and then there can be subtle deanonymization edge cases but they don't scale). It reminds me the FDA saying they can't release the COVID-19 documents because reviewing 44'000 documents would take 50 years. It didn't take 50 years to produce them... Yes there is some effort needed to anonymize reasonably the data but it's not an impossible task. It's a question of motivation. Here, clearly, the labs and administration don't really want to put efforts into that.
  - throwawaygh 5y ago
    Presumable FDAs analysis assumed current staffing levels. Going to go out on a limb and assume they’ve got a LOT more people involved in creating docs than in deidentifying docs. And, yes, I think public data on this sort of stuff is important and should be properly resourced. I think: Step 1. ASK PERMISSION before changing the way data is handled. Step 2. Share full datasets more generously, but still gated by use and handling agreements. This probably means a private citizens without ethics research training and a supporting it dept can’t get a copy and peruse it on their personal laptop, but also that a truly enormous number of researchers would be able to access the data. The gold standard of a CSV in a public s3 bucket shouldn’t be the enemy of good enough.
jjulius 5y ago
I'm not so sure that you should be so sure that there are no databases that such data can be referenced against. Regarding stripping out major identifiers, please note that OP commented that "it's not as simple as just removing the sensitive medical data because the primary or secondary analyses may be dependent on them". And of course raw data like this could benefit patients, but keeping access to raw data limited also benefits patients. Sure, the data is readily available under a loose NDA, but it's available to people who have explicit knowledge of the requirements around handling sensitive, identifiable data. Average Joe's and Jane's do not have this knowledge, and bad actors just plain don't give a shit.
ashtonkem 5y ago
I mean, it’s not like anonymous datasets haven’t been de-anonymized before[0]. Successfully anonymizing data sets is a hard and subtle process, and it’s way harder than just removing major identifiers like city and birth date. For example age is obviously super important for vaccine and disease studies, and providing an age narrows down someone’s birthdate significantly. And no, this isn’t under a “loose” NDA. This would be covered by HIPAA, which tends to be un-subtle about violations. 0 - https://www.cs.princeton.edu/~arvindn/publications/de-anonymization-retrospective.pdf https://www.cs.princeton.edu/~arvindn/publications/de-anonym...
hcknwscommenter 5y ago
"There are no databases that you can link against if you strip out the major identifiers" Isn't that provably untrue? https://bits.blogs.nytimes.com/2015/01/29/with-a-few-bits-of-data-researchers-identify-anonymous-people/ https://bits.blogs.nytimes.com/2015/01/29/with-a-few-bits-of...