OpenSAFELY Update – July 2024

Dear OpenSAFELY Users,

There have been a number of significant changes to the NHS England (NHSE) OpenSAFELY service and governance recently. Unfortunately some of these changes mean that the service is effectively - temporarily - closed at this time. While we are confident that the service will re-open in the near future, we wanted to write to explain, and to give a wider update, including on all the positive things coming shortly to the platform.

Type 1 Opt-Outs

As you know, we completed a significant piece of work earlier this year, to ensure that OpenSAFELY would honour the wishes of everyone who has registered a Type 1 Opt-Out (T1OO).

As a number of projects were underway in the service at that time, and were using that data as permitted by the emergency legislation introduced during the pandemic, these “Transitional” projects were given permission to conclude their work. The majority of these projects completed their work as scheduled, by June, but a small number requested additional time to analyse data, primarily to respond to peer-review comments – NHSE considered all such requested, and have granted some projects permission to continue until the end of the year, but only on the condition that this work excludes data for people registering a T1OO. All project leads who requested an extension will receive details of this by the end of this week.

After implementing the change to honour T1OOs for all future uses of OpenSAFELY, we identified a small potential gap: it is not possible to identify whether patients who have moved between EHR system suppliers have subsequently registered a T1OO (e.g. a patient moves from a TPP surgery to an EMIS surgery and then registers an opt-out in the EMIS surgery. In this scenario, TPP won’t know which of the patients who have now moved to EMIS, have registered a T1OO: the systems do not currently share this information). We are working rapidly on proposing a long-term solution to this, and intend to formally present that solution to the NHSE OpenSAFELY Steering Group and the Joint GP IT Committee in September.

To be cautious and ensure we fully honour all opt-outs, we are introducing an interim solution - we will remove all patients who have moved from TPP to EMIS (or vice-versa) from the accessible data for users. No analyses can be run until this change has been made, which we anticipate being made and tested before the end of this month.

We are happy to discuss this with users, and any possible impact on analyses: however, a benefit of OpenSAFELY is that users can develop and run their code on the current data, then easily re-run it later when this issue is addressed to establish whether their results were affected.

Formal agreements with the GP System Suppliers

NHSE are currently working with the GP System Suppliers (TPP and EMIS) on the formal agreements necessary to govern their continued support for the service. The service requires a commercial agreement between NHSE and each supplier, to cover their costs to support OpenSAFELY, and a Data Processing Agreement (DPA) to document how data should be managed. While this is ongoing the TPP half of the service will remain open, but the EMIS half of the service will remain closed.

NHSE are in the final stages of implementing a new DPA with TPP, which should be in place imminently – at that point, the TPP half of the service will be able to restart, and NHSE will focus on finalising a DPA with EMIS. Until they conclude this work with TPP, unfortunately, no new project analyses can run in OpenSAFELY-TPP.

Analytical Methods Policy

You may have seen that we have recently introduced a new policy, which sets out the analytical methods that can be used in OpenSAFELY. This policy aims to manage two limitations imposed upon us by external factors: we can’t pay for additional compute to support certain machine learning methods; and some machine learning analytic methods present privacy challenges around secure output checking that have not yet been resolved by any teams anywhere, and therefore cannot yet be implemented in a dataset with total population coverage. We anticipate that this policy will be refreshed and updated over the coming months: we would welcome feedback on it, and suggested changes that could simplify work for researchers while maintaining patients’ privacy, and addressing the additional challenges, for example, around interpretability, explainability and safety of these methods. Maintaining the trust of the public and the profession is a key priority for teams running the OpenSAFFELY COVID-19 service .

We have recently written to all study leads with a current project, asking them to briefly confirm that their project will adhere to this policy, and require a response before those projects can restart. We will update the application form and Data Access Agreement to make this requirement clear for future work.

Non-Covid Uses of OpenSAFELY

Much more positively, we are continuing to progress work on access to GP data through OpenSAFELY for analyses beyond COVID-19, as announced by NHSE in November (link to NHSE announcement); progress is extremely good, and our primary focus, other than resolving the current barriers to use, is on ensuring the service is ready to support this significant expansion. The GP profession (the BMA and RCGP) also continues to provide strong support for the use of OpenSAFELY beyond COVID-19 purposes. We expect to have news in the coming months.

Recent Outputs

Despite the changes introduced this year, and the current restrictions on access to the service, the NHS England OpenSAFELY Service continues to be highly productive, thanks principally to your outstanding work. Some recently published papers are listed below, which help demonstrate the enduring value of the service, and the potential of what we can collectively achieve once current issues are resolved and new projects addressing important questions beyond COVID-19 can be approved:

Curation of GP ethnicity data
https://www.bennett.ox.ac.uk/papers/10.1186/s12916-024-03499-5/

Fit notes activity for COVID
https://www.bennett.ox.ac.uk/papers/10.1136/bmjopen-2023-080600/

Vaccine Effectiveness
https://www.bennett.ox.ac.uk/papers/10.1097/ede.000000000000174/

Real time reporting for Strep C outbreak
https://www.bennett.ox.ac.uk/papers/10.1136/bmjmed-2023-000791/

Trends and variation opioids during COVID
https://www.bennett.ox.ac.uk/papers/10.1016/s2468-26672400100-2/

Weight gain during COVID
https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1004398

OpenPrompt - incorporating smartphone application data within OpenSAFELY to collect quality of life information
https://www.thelancet.com/journals/lanepe/article/PIIS2666-7762(24)00074-7/fulltext

Risk of emergency hospital admission after antibiotic treatment
https://pubmed.ncbi.nlm.nih.gov/38956603/

Antibiotic Exposure Characteristics for COVID-19 Hospital Admission
https://pubmed.ncbi.nlm.nih.gov/38927232/

OpenSAFELY Symposium

Following our inaugural conference last year, we will be holding an OpenSAFELY symposium on 25-26 November.

The symposium will be two days of talks and workshops on OpenSAFELY, data infrastructure, and open science, and we hope as many of you as possible will be able to join us.

Please register for the conference on November 25th and 26th using our EventBrite link. If you would like to speak or run a workshop we would be delighted and are currently accepting suggestions using our online form.

When can you start work again?

Once we have implemented the interim solution for patients who have moved between EMIS and TPP (see T1OO heading above), and NHSE have finalised the DPA with TPP, the OpenSAFELY service will re-open in TPP for all existing projects (including those approved this year but not yet started, and those Transitional projects given an extension until the end of December). Researchers on those projects will be able to start/resume work as soon as they have confirmed adherence to the Analytical Methods Policy. We are confident that we will re-open in the very near future.

The OpenSAFELY-EMIS service will take longer to restart, as this requires completion of the commercial agreement between NHSE and EMIS.

In the meantime, NHSE are now happy to receive and review new applications to use OpenSAFELY (for Covid-19 related research, in TPP, initially), so please do submit your proposals using the online application or contact us to discuss further.