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How OpenSAFELY makes reproducible research easier

We describe the features of OpenSAFELY that encourage and support reproducible research.

DMARD monitoring during the COVID-19 pandemic

We describe some of our recent work investigating the impact of the COVID-19 pandemic on DMARD safety monitoring across >24 million patients’ records in England.

OpenSAFELY research software advocate vacancy

We’re hiring a research software advocate and we think you’d be a good fit

OpenSAFELY software engineering vacancies

We’re hiring software people and we’d love you to join us

The impact of COVID-19 on medication reviews in English primary care. An OpenSAFELY analysis. Part 2: Results

In the second of a two-part blog series, pharmacists Chris Wood and Vicky Speed talk about the results of their research on medication review activity

The impact of COVID-19 on medication reviews in English primary care. An OpenSAFELY analysis. Part 1: Analysis Design

In the first of a two-part blog series, pharmacists Chris Wood and Vicky Speed talk about designing their research on medication review activity

Research vacancies

We’re hiring for our research teams

The OpenSAFELY tech teams' work pipeline

How we organize and plan work for our tech teams

Ben Goldacre appears on BBC's More or Less

Ben discusses the OpenSAFELY platform with fellow nerd Tim Harford

OpenPrescribing Winter 2023/2024 Newsletter

This newsletter contains all the latest updates from OpenPrescribing

PINCER: Monitoring medication safety throughout the COVID-19 pandemic using OpenSAFELY

Here we describe some of our recent work investigating the impact of the COVID-19 pandemic on safe prescribing using a set of quality assured indicators across 57 million patients’ records in England

Trends in inequalities in avoidable hospitalisations across the COVID-19 pandemic

In this guest blog, Mark Green describes their latest paper using OpenSAFELY.

How we test ehrQL

How can you be confident that the queries you write will be correctly interpreted and return the expected results?

Bennett Conference session 4: OpenSAFELY research highlights, external perspectives & Peter Bennett

The final session was a series of talks highlighting some of the research conducted in OpenSAFELY, some external perspectives on OpenSAFELY, and concluding remarks from our benefactor Peter Bennett, and director Ben Goldacre.

Bennett Conference session 3: How OpenSAFELY Works

The third session in the Bennett Conference was a series of talks describing the overall operation of the OpenSAFELY platform and service.

Understanding Repeat Antibiotic Prescribing in the Pandemic: Insights On Health Inequalities

The COVID-19 pandemic has reshaped many aspects of healthcare, including how antibiotics are prescribed in primary care settings. In this guest blog, Professor Diane Ashiru-Oredope lead pharmacist for antimicrobial resistance at UK Health Security Agency and our own Brian MacKenna, share some insights on repeat antibiotic prescribing and the link to health inequalities from a recent UK Health Security Agency analysis using OpenSAFELY.

The future of OpenSAFELY: an important announcement from NHS England, DHSC and the Bennett Institute at Oxford

We are delighted to share the announcement from NHS England and Department of Health and Social Care below, setting out the future of OpenSAFELY.

Updates of OpenSAFELY Research on COVID-19 Therapeutics

In this guest blog, Bang Zheng and Laurie Tomlinson from the London School of Hygiene and Tropical Medicine describe some of their lastest work on the comparative effectiveness and safety of currently recommended COVID-19 therapeutics in the community settings.

OpenPrescribing Autumn 2023 Newsletter

OpenPrescribing Autumn 2023 Newsletter.

Incidence and management of inflammatory arthritis in England before and during the COVID-19 pandemic

In this guest blog, Mark Russell describes the research that he has undertaken with the help of his team from King’s College London using OpenSAFELY.

Exploring the Impact of COVID-19 on common infections: Treatment Pathways, Antibiotic Prescribing, and Exposure

Xiaomin Zhong, Ya-Ting Yang, Dr Ali Fahmi, Dr Victoria Palin and Professor Tjeerd Van Staa from Manchester University have been using OpenSAFELY for analyses focused on the impact of COVID-19 on antimicrobial resistance since 2021. In this guest blog they describe some of their recent papers that have been published in peer review journals.

Unlocking Discoveries Safely: Using the primary care data of 59 million patients to determine the impact of the COVID-19 pandemic on antipsychotic prescribing in at-risk populations

In this blog post Millie Green shares some of the findings from a federated analysis carried out using OpenSAFELY.

What Are Codelists and How Are They Constructed?

In this blog we explain what codelists are, how they are constructed and review existing literature on construction processes.

Why ehrQL?

Why did we create a new query language?

OpenSAFELY Wins CogX Award for Open Science Innovation

The OpenSAFELY Collaborative has won a prestigious CogX Award for the Best Innovation in Open Source Technology

OpenSAFELY Service Restoration Observatory: Key Measures

In this blog, we describe the development of a set of key measures used to monitor the ongoing impact of the COVID-19 pandemic on primary care as part of the OpenSAFELY Service Restoration Observatory (SRO). The results from this work have now been published in eLife.

Introduction to the Information Governance Team

Here we introduce the Bennett Institute’s Information Governance team, explaining who they are, and what they do.

Challenges in Estimating COVID-19 Vaccine Effectiveness Using Observational Data

Our new paper describes some of the biases that exist when estimating COVID-19 vaccine effectiveness using routinely-collected health data, and discusses the use of target trial emulation to avoid or mitigate these biases.

An Introduction to Clinical Codes and Terminology Systems

An introduction to what clinical codes are, why they are used and the terminology systems used within OpenSAFELY work.

Running the OpenSAFELY Output Checking Service

A summary of our findings from running the OpenSAFELY output checking service.

OpenSAFELY for Impact: COVID-19 Therapeutics

Millie and Laurie share how some of the outputs from the work on COVID-19 therapeutics have been used to inform policy and guidelines in the NHS and beyond.

NHS Service Restoration Observatory 2: changes in primary care clinical activity in England during the COVID-19 pandemic

The latest paper from our NHS Service Restoration Observatory, examining changes in primary care activity over the pandemic was recently published in the British Journal of General Practice.

Introduction to the Product Team

The OpenSAFELY Product Team’s mission is to understand our users’ needs, identify opportunities to improve OpenSAFELY products, and work with the tech teams to figure out the best solutions to build. Who are we? Catherine Stables is Lead Product Manager. In her previous role she was Data Product Manager for DataLoch, based at the University of Edinburgh. She has a background in academic research on cardiovascular disease, and a PhD from King’s College London.

COVID-19-related mortality from 2020 to 2022: the changing picture

Our OpenSAFELY study describing patterns in COVID-19-related mortality in the first five pandemic waves is now published open-access in the Lancet Public Health.

The Opensafely Output Checking Service

An outline the OpenSAFELY output checking service: who it involves, how our output checkers are trained and an overview of the output checking workflow.

Introduction to the Pipeline Team

Introducing the Bennett Institute’s Pipeline team, where we talk about who we are, what we do and some of the products we’re responsible for.

Introduction to the NHS Service Analytics Team

Here we introduce the Bennett Institute’s NHS Service Analytics team, explaining who they are, what they do, and why it is important.

Introduction to the Epidemiology Team

Here we introduce the Bennett Institute’s Epidemiology team, explaining who they are, what they do, and why it is important.

Comparative Effectiveness of Pfizer and Moderna COVID-19 Vaccines for Boosting

Our OpenSAFELY study comparing the Pfizer and Moderna vaccines for protecting against covid-19 during the first booster programme in England is now published open-access in the BMJ.

Introduction to the Clinical Informatics Team

Here we introduce the Bennett Institute’s Clinical Informatics team, explaining what they do and how their experience in NHS clinical practice helps them do this.

Introduction to the Data Team

Hello, from the Bennett Institute’s Data Team! In this short blog post, we’ll describe our mission, our backgrounds in industry and academia, and what we’re working on now.

An Update on Our Co-piloting Programme: How Have We Grown?

Taking some time to describe the co-piloting programme in numbers, to give an idea of the scale of this programme, who our co-pilots are and who we are working with

Re-running your study, quickly and easily: why automated pipelines matter for research

Better and more efficient health science with reusable pipelines and cross-disciplinary expertise.

‘Safe Outputs’ and Statistical Disclosure Control in OpenSAFELY

Taking a deeper look at the ‘Safe Outputs’ dimension of this framework, and how it is applied in OpenSAFELY.

OpenSAFELY Research Highlights

Here we outline some of the research that has been produced with OpenSAFELY, as well as the features that make it such a great platform for research.

The ‘Five Safes’ Framework and applying it to OpenSAFELY

The Fives Safes framework is a popular framework for designing safe and efficient data access systems that has been adopted by a range of Trusted Research Environments (TREs) across the UK.

OpenSAFELY NHS Service Analytics

On 7th May 2020, the OpenSAFELY Collaborative pre-printed the world’s largest study into factors associated with death from COVID-19, based on an analysis running across the full pseudonymised health records of 40% of the English population.

Generating data on the NHS England Core20PLUS5 inequality groups using OpenSAFELY in GP records

In order to tackle health inequalities NHS England have recently launched the Core20PLUS5 initiative to help local areas identify and reduce inequalities across key areas.

Using electronic health records and open science in the COVID-19 pandemic

We recently presented on behalf of our team (grp-EHR) at an open science workshop, hosted by the MRC Biostatistics Unit at the University of Cambridge. This was a great opportunity for us to reflect on our team’s experiences using OpenSAFELY, and more broadly embracing open and team science approaches to our work.

An Update on Our Co-piloting Programme: What's New?

As a team of co-pilots, we regularly take time to discuss how co-piloted projects are going and what we can do to help pilots and co-pilots make the most of their time together.

Conducting Research Using OpenSAFELY: My Experience of the Co-pilot Service

Rachel Seeley is the Head of Analytics at PrescQIPP CIC and has recently completed a project in OpenSAFELY on the safer use of anticoagulant medication. In this guest blog, Rachel describes her experience with using the OpenSAFELY platform and our co-pilot programme.

Difference between BNF, dm+d and SNOMED CT codes

Bennett Institute resident pharmacist Brian MacKenna sets out some brief information on how we currently build medicines codelists on OpenSAFELY.

OpenPrescribing June 2022 Newsletter

Our latest newsletter including information on: Bennett Institute for Applied Data Science, we are recruiting, Goldacre Review, updated Outlier Dashboards, recent changes to OpenPrescribing Measures, OpenSAFELY news, and new data news.

Invitation: CIPHA-OpenSAFELY Introduction Event

CIPHA and OpenSAFELY are hosting an introduction event for researchers in the North West of England who would like to work with CIPHA data using OpenSAFELY.

Closing the STEM gap is a collective responsibility

Our policy lead, Jess Morley, discusses the challenges involved in closing the gap in representation and reward for women working in these fields, and what we in the Bennett Institute are trying to do to help lower some of the associated barriers.

OpenPrescribing December Newsletter

Our latest newsletter including information on: We are recruiting, recent changes to OpenPrescribing Measures, new Outlier Prescribing tool, maps update, recent research publications, OpenSAFELY news, and new data news.

First Impressions of a New Start

I joined Bennett Institute in August 2021 to work as a data scientist on OpenSAFELY. This blog post describes my experience getting up and running with the OpenSAFELY pipeline.

Exploring automated output checking with OpenSAFELY

This is a guest blog from the team at Cantabular, who have been exploring how their technology might fit into the OpenSAFELY ecosystem.

OpenSAFELY co-pilot programme: assisting users on their OpenSAFELY journey

All new users of the OpenSAFELY platform get access to our supportive co-pilot programme, where each new OpenSAFELY user is assigned a member of the OpenSAFELY team as their co-pilot for the duration of their project.

OpenSAFELY: Public Opinion

This week sees the publication of an independent Citizens’ Jury commissioned for NHSx and the National Data Guardian which found that OpenSAFELY was by far the most strongly and consistently supported of all NHS COVID data projects examined.

OpenSAFELY: The Origin Story

On our first anniversary, from the Policy Lead in the Bennett Institute, this is the brief story of the positive side from all our lives: how OpenSAFELY came to life, and what we’ve achieved so far.

Citing and Crediting Codelists: A discussion for the research community

This is a draft discussion paper, the first of a series exploring “open team science” approaches to managing health data, and specifically how to create a collaborative computational data science ecosystem where the sharing and re-use of objects such as codelists and code is facilitated, encouraged, recognised, and rewarded. As a microcosm of this we have first explored “codelists”. There are currently no ‘answers’ or preferred solutions given. We will be holding an open discussion with the research community on 2nd March at 3pm - you can book to join us here.

OpenPrescribing Newsletter November 2020

We have been very busy since our last newsletter back in July and there are tonnes of exciting updates for you here! Measure Update: Total Oral Morphine Equivalence The Faculty of Pain Medicine has recently updated their recommendation on oral morphine equivalence (OME) which we use on our OpenPrescribing measure of OME. We have taken this opportunity to update and a new novel implementation of how we assess OME. Until this work is completed we have taken the decision to “suspend” the measure from dashboards however you can still view the old method using this link.

OpenSAFELY Cohort Extractor

This is the code for the OpenSAFELY cohort extractor tool which supports the authoring of OpenSAFELY-compliant research, by: Allowing developers to generate random data based on their study expectations. They can then use this as input data when developing analytic models. Supporting downloading of codelist CSVs from the OpenSAFELY codelists repository, for incorporation into the study definition Providing tools to understand and visualise the properties of real data, without having direct access to it It is also the mechanism by which cohorts are extracted from live database backends within the OpenSAFELY framework.

OpenSAFELY Job Runner

This is the repository for the OpenSAFELY job runner. A job runner is a service that encapsulates: the task of checking out an OpenSAFELY study repo; executing actions defined in its project.yaml configuration file when requested via a jobs queue; and storing its results in a particular locations. The documentation is aimed at developers looking for an overview of how the system works. It also has some parts relevant for end users, particularly the project.

OpenSAFELY Job Server

This is the code for the OpenSAFELY job server designed for mediating jobs that can be run in an OpenSAFELY secure environment. The Django app provides a simple REST API which provides a channel for communicating between low-security environments (which can request that jobs be run) and high-security environments (where jobs are run).

What is OpenSAFELY?

What is OpenSAFELY? Working on behalf of NHS England we have now built a full, open source, highly secure analytics platform running across the full pseudonymised primary care records of 24 million people, rising soon to 55 million, 95% of the population of England. We have pursued a new model: for privacy, security, low cost, and near-real-time data access, we have built the analytics platform inside the EHR data centre of the major EHR providers, where the data already resides; in addition we have built software that uses tiered increasingly non-disclosive tables to prevent researchers ever needing direct access to the disclosive underlying data to run analyses; code is developed against simulated data using open platforms before moving to the live data environment.

OpenPrescribing July Newsletter

OpenPrescribing and Bennett Institute Papers It has been a busy month for paper publication at The Bennett Institute. We have written a brief description of the most recent papers below. Please sharewith colleagues and get in touch if you have any relevant observations! Remember you can read all our academic papers related to OpenPrescribing on our research page. Hospital medicines data: We are frequently contacted at OpenPrescribing about when we are going to make a hospital version.

OpenPrescribing June Newsletter

Methotrexate Prescribing Safety — New paper in BJGP This week the British Journal of General Practice published our latest paper on unsafe prescribing of methotrexate. We found that the prevalence of unsafe methotrexate prescribing (10mg tablets) has reduced but remains common, with substantial variation between practices and CCGs. In the paper we also discuss recommendations for better strategies around implementation. Anyone can view the live data on unsafe methotrexate prescribing at openprescribing.

OpenPrescribing Newsletter May 2020

OpenSAFELY.org OpenSAFELY is a new secure analytics platform for electronic health records in the NHS, created to deliver urgent results during the global COVID-19 emergency. OpenSAFELY is a collaboration between the Bennett Institute, the EHR group at London School of Hygiene and Tropical Medicine and TPP who produce SystmOne. OpenSAFELY is now successfully delivering analyses across more than 24 million patients’ full pseudonymised primary care NHS records. The first analysis from OpenSAFELY is Factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients with more answers to important questions expected shortly.

Impact of COVID-19 on prescribing in English general practice: March 2020

OpenPrescribing.net has been updated this week with the latest release of prescribing data covering March 2020. In-depth analysis will be needed over the coming months, but this release gives us the first glimpse into the impact that COVID-19 has had on prescribing. At the Bennett Institute we have been quite busy with the new secure analytics platform OpenSAFELY but the following blog is a rapid analysis of the March prescribing data which others may find helpful to focus their own investigations.