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      Biosecurity in an age of open science

      review-article
      1 , 2 , * , , 3 , 4 , * ,
      PLoS Biology
      Public Library of Science

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          Abstract

          The risk of accidental or deliberate misuse of biological research is increasing as biotechnology advances. As open science becomes widespread, we must consider its impact on those risks and develop solutions that ensure security while facilitating scientific progress. Here, we examine the interaction between open science practices and biosecurity and biosafety to identify risks and opportunities for risk mitigation. Increasing the availability of computational tools, datasets, and protocols could increase risks from research with misuse potential. For instance, in the context of viral engineering, open code, data, and materials may increase the risk of release of enhanced pathogens. For this dangerous subset of research, both open science and biosecurity goals may be achieved by using access-controlled repositories or application programming interfaces. While preprints accelerate dissemination of findings, their increased use could challenge strategies for risk mitigation at the publication stage. This highlights the importance of oversight earlier in the research lifecycle. Preregistration of research, a practice promoted by the open science community, provides an opportunity for achieving biosecurity risk assessment at the conception of research. Open science and biosecurity experts have an important role to play in enabling responsible research with maximal societal benefit.

          Abstract

          The risk of biotechnology being misused is growing and may even be increased by moves towards open science. How can we ensure that the goals of both open science and biosecurity are met?

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          Most cited references80

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          The FAIR Guiding Principles for scientific data management and stewardship

          There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
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            OpenSAFELY: factors associated with COVID-19 death in 17 million patients

            COVID-19 has rapidly impacted on mortality worldwide. 1 There is unprecedented urgency to understand who is most at risk of severe outcomes, requiring new approaches for timely analysis of large datasets. Working on behalf of NHS England we created OpenSAFELY: a secure health analytics platform covering 40% of all patients in England, holding patient data within the existing data centre of a major primary care electronic health records vendor. Primary care records of 17,278,392 adults were pseudonymously linked to 10,926 COVID-19 related deaths. COVID-19 related death was associated with: being male (hazard ratio 1.59, 95%CI 1.53-1.65); older age and deprivation (both with a strong gradient); diabetes; severe asthma; and various other medical conditions. Compared to people with white ethnicity, black and South Asian people were at higher risk even after adjustment for other factors (HR 1.48, 1.29-1.69 and 1.45, 1.32-1.58 respectively). We have quantified a range of clinical risk factors for COVID-19 related death in the largest cohort study conducted by any country to date. OpenSAFELY is rapidly adding further patients’ records; we will update and extend results regularly.
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              Data Resource Profile: Clinical Practice Research Datalink (CPRD)

              The Clinical Practice Research Datalink (CPRD) is an ongoing primary care database of anonymised medical records from general practitioners, with coverage of over 11.3 million patients from 674 practices in the UK. With 4.4 million active (alive, currently registered) patients meeting quality criteria, approximately 6.9% of the UK population are included and patients are broadly representative of the UK general population in terms of age, sex and ethnicity. General practitioners are the gatekeepers of primary care and specialist referrals in the UK. The CPRD primary care database is therefore a rich source of health data for research, including data on demographics, symptoms, tests, diagnoses, therapies, health-related behaviours and referrals to secondary care. For over half of patients, linkage with datasets from secondary care, disease-specific cohorts and mortality records enhance the range of data available for research. The CPRD is very widely used internationally for epidemiological research and has been used to produce over 1000 research studies, published in peer-reviewed journals across a broad range of health outcomes. However, researchers must be aware of the complexity of routinely collected electronic health records, including ways to manage variable completeness, misclassification and development of disease definitions for research.
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                Author and article information

                Journal
                PLoS Biol
                PLoS Biol
                plos
                PLoS Biology
                Public Library of Science (San Francisco, CA USA )
                1544-9173
                1545-7885
                14 April 2022
                April 2022
                14 April 2022
                : 20
                : 4
                : e3001600
                Affiliations
                [1 ] Botnar Research Centre and Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
                [2 ] National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
                [3 ] Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
                [4 ] Future of Humanity Institute, University of Oxford, Oxford, United Kingdom
                Author notes

                I have read the journal’s policy and the authors of this manuscript have the following competing interests: in 2017 James Smith was a consultant for Biolacuna Ltd. He is currently a consultant to Alvea LLC/Telis Bioscience Inc.

                Author information
                https://orcid.org/0000-0003-2634-0268
                Article
                PBIOLOGY-D-21-03244
                10.1371/journal.pbio.3001600
                9009689
                35421093
                95fb38fc-9036-4147-9770-23d26c5eb28f
                © 2022 Smith, Sandbrink

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Page count
                Figures: 1, Tables: 0, Pages: 14
                Funding
                Funded by: Effective Altriusm funds via the Long Term Future Fund
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100013373, NIHR Oxford Biomedical Research Centre;
                Award Recipient :
                Funded by: Open Philanthropy
                Award Recipient :
                JAS received support from the Effective Altruism Funds programme via the Long Term Future Fund ( https://funds.effectivealtruism.org/funds/far-future). JAS’s postdoctoral position is funded by the Oxford National Institute for Health Research Biomedical Research Centre ( https://oxfordbrc.nihr.ac.uk/). JBS's doctoral research is funded by Open Philanthropy ( https://www.openphilanthropy.org/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Essay
                Science Policy
                Open Science
                Medicine and Health Sciences
                Epidemiology
                Medical Risk Factors
                Biology and Life Sciences
                Bioengineering
                Engineering and Technology
                Bioengineering
                Medicine and Health Sciences
                Epidemiology
                Pandemics
                Research and Analysis Methods
                Research Assessment
                Peer Review
                Biology and Life Sciences
                Bioengineering
                Biotechnology
                Genetic Engineering
                Engineering and Technology
                Bioengineering
                Biotechnology
                Genetic Engineering
                Research and Analysis Methods
                Research Assessment
                Biology and Life Sciences
                Microbiology
                Microbial Control
                Antimicrobial Resistance
                Antibiotic Resistance
                Medicine and Health Sciences
                Pharmacology
                Antimicrobial Resistance
                Antibiotic Resistance

                Life sciences
                Life sciences

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