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Kępińska AP, Johnson JS, Huckins LM. Open Science Practices in Psychiatric Genetics: A Primer. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:110-119. [PMID: 38298792 PMCID: PMC10829621 DOI: 10.1016/j.bpsgos.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 02/02/2024] Open
Abstract
Open science ensures that research is transparently reported and freely accessible for all to assess and collaboratively build on. Psychiatric genetics has led among the health sciences in implementing some open science practices in common study designs, such as replication as part of genome-wide association studies. However, thorough open science implementation guidelines are limited and largely not specific to data, privacy, and research conduct challenges in psychiatric genetics. Here, we present a primer of open science practices, including selection of a research topic with patients/nonacademic collaborators, equitable authorship and citation practices, design of replicable, reproducible studies, preregistrations, open data, and privacy issues. We provide tips for informative figures and inclusive, precise reporting. We discuss considerations in working with nonacademic collaborators and distributing research through preprints, blogs, social media, and accessible lecture materials. Finally, we provide extra resources to support every step of the research process.
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Affiliation(s)
- Adrianna P. Kępińska
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Jessica S. Johnson
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
- Psychiatry Department, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Laura M. Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychiatry, Yale University, New Haven, Connecticut
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Blatch-Jones AJ, Recio Saucedo A, Giddins B. The use and acceptability of preprints in health and social care settings: A scoping review. PLoS One 2023; 18:e0291627. [PMID: 37713422 PMCID: PMC10503772 DOI: 10.1371/journal.pone.0291627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Preprints are open and accessible scientific manuscript or report that is shared publicly, through a preprint server, before being submitted to a journal. The value and importance of preprints has grown since its contribution during the public health emergency of the COVID-19 pandemic. Funders and publishers are establishing their position on the use of preprints, in grant applications and publishing models. However, the evidence supporting the use and acceptability of preprints varies across funders, publishers, and researchers. The scoping review explored the current evidence on the use and acceptability of preprints in health and social care settings by publishers, funders, and the research community throughout the research lifecycle. METHODS A scoping review was undertaken with no study or language limits. The search strategy was limited to the last five years (2017-2022) to capture changes influenced by COVID-19 (e.g., accelerated use and role of preprints in research). The review included international literature, including grey literature, and two databases were searched: Scopus and Web of Science (24 August 2022). RESULTS 379 titles and abstracts and 193 full text articles were assessed for eligibility. Ninety-eight articles met eligibility criteria and were included for full extraction. For barriers and challenges, 26 statements were grouped under four main themes (e.g., volume/growth of publications, quality assurance/trustworthiness, risks associated to credibility, and validation). For benefits and value, 34 statements were grouped under six themes (e.g., openness/transparency, increased visibility/credibility, open review process, open research, democratic process/systems, increased productivity/opportunities). CONCLUSIONS Preprints provide opportunities for rapid dissemination but there is a need for clear policies and guidance from journals, publishers, and funders. Cautionary measures are needed to maintain the quality and value of preprints, paying particular attention to how findings are translated to the public. More research is needed to address some of the uncertainties addressed in this review.
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Affiliation(s)
- Amanda Jane Blatch-Jones
- National Institute for Health and Care Research (NIHR) Coordinating Centre, School of Healthcare Enterprise and Innovation, University of Southampton, Southampton, Hampshire, United Kingdom
| | - Alejandra Recio Saucedo
- National Institute for Health and Care Research (NIHR) Coordinating Centre, School of Healthcare Enterprise and Innovation, University of Southampton, Southampton, Hampshire, United Kingdom
| | - Beth Giddins
- National Institute for Health and Care Research (NIHR) Coordinating Centre, School of Healthcare Enterprise and Innovation, University of Southampton, Southampton, Hampshire, United Kingdom
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Haven T, Gopalakrishna G, Tijdink J, van der Schot D, Bouter L. Promoting trust in research and researchers: How open science and research integrity are intertwined. BMC Res Notes 2022; 15:302. [PMID: 36127719 PMCID: PMC9487848 DOI: 10.1186/s13104-022-06169-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
Proponents of open science often refer to issues pertaining to research integrity and vice versa. In this commentary, we argue that concepts such as responsible research practices, transparency, and open science are connected to one another, but that they each have a different focus. We argue that responsible research practices focus more on the rigorous conduct of research, transparency focuses predominantly on the complete reporting of research, and open science's core focus is mostly about dissemination of research. Doing justice to these concepts requires action from researchers and research institutions to make research with integrity possible, easy, normative, and rewarding. For each of these levels from the Center for Open Science pyramid of behaviour change, we provide suggestions on what researchers and research institutions can do to promote a culture of research integrity. We close with a brief reflection on initiatives by other research communities and stakeholders and make a call to those working in the fields of research integrity and open science to pay closer attention to one other's work.
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Affiliation(s)
- Tamarinde Haven
- BIH QUEST Center for Responsible Research, Charité Universitätsmedizin, Berlin, Germany.
| | - Gowri Gopalakrishna
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Joeri Tijdink
- Department of Ethics, Law and Humanities, Amsterdam University Medical Centers, Amsterdam, the Netherlands.,Department of Philosophy, Faculty of Humanities, Vrije Universiteit, Amsterdam, Netherlands
| | - Dorien van der Schot
- Department of Philosophy, Faculty of Humanities, Vrije Universiteit, Amsterdam, Netherlands
| | - Lex Bouter
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Amsterdam, The Netherlands.,Department of Philosophy, Faculty of Humanities, Vrije Universiteit, Amsterdam, Netherlands
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Grant S, Wendt KE, Leadbeater BJ, Supplee LH, Mayo-Wilson E, Gardner F, Bradshaw CP. Transparent, Open, and Reproducible Prevention Science. PREVENTION SCIENCE : THE OFFICIAL JOURNAL OF THE SOCIETY FOR PREVENTION RESEARCH 2022; 23:701-722. [PMID: 35175501 PMCID: PMC9283153 DOI: 10.1007/s11121-022-01336-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 01/20/2023]
Abstract
The field of prevention science aims to understand societal problems, identify effective interventions, and translate scientific evidence into policy and practice. There is growing interest among prevention scientists in the potential for transparency, openness, and reproducibility to facilitate this mission by providing opportunities to align scientific practice with scientific ideals, accelerate scientific discovery, and broaden access to scientific knowledge. The overarching goal of this manuscript is to serve as a primer introducing and providing an overview of open science for prevention researchers. In this paper, we discuss factors motivating interest in transparency and reproducibility, research practices associated with open science, and stakeholders engaged in and impacted by open science reform efforts. In addition, we discuss how and why different types of prevention research could incorporate open science practices, as well as ways that prevention science tools and methods could be leveraged to advance the wider open science movement. To promote further discussion, we conclude with potential reservations and challenges for the field of prevention science to address as it transitions to greater transparency, openness, and reproducibility. Throughout, we identify activities that aim to strengthen the reliability and efficiency of prevention science, facilitate access to its products and outputs, and promote collaborative and inclusive participation in research activities. By embracing principles of transparency, openness, and reproducibility, prevention science can better achieve its mission to advance evidence-based solutions to promote individual and collective well-being.
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Affiliation(s)
- Sean Grant
- Department of Social & Behavioral Sciences, Fairbanks School of Public Health, Indiana University Richard M, 1050 Wishard Blvd, Indianapolis, IN, 46202, USA.
| | - Kathleen E Wendt
- Department of Human Development and Family Studies, Colorado State University, Fort Collins, CO, USA
| | | | | | - Evan Mayo-Wilson
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA
| | - Frances Gardner
- Department of Social Policy and Intervention, University of Oxford, Oxford, UK
| | - Catherine P Bradshaw
- School of Education & Human Development, University of Virginia, Charlottesville, VA, USA
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Higgins SG, Nogiwa-Valdez AA, Stevens MM. Considerations for implementing electronic laboratory notebooks in an academic research environment. Nat Protoc 2022; 17:179-189. [PMID: 35031789 DOI: 10.1038/s41596-021-00645-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/07/2021] [Indexed: 11/09/2022]
Abstract
As research becomes predominantly digitalized, scientists have the option of using electronic laboratory notebooks to record and access entries. These systems can more readily meet volume, complexity, accessibility and preservation requirements than paper notebooks. Although the technology can yield many benefits, these can be realized only by choosing a system that properly fulfills the requirements of a given context. This review explores the factors that should be considered when introducing electronic laboratory notebooks to an academically focused research group. We cite pertinent studies and discuss our own experience implementing a system within a multidisciplinary research environment. We also consider how the required financial and time investment is shared between individuals and institutions. Finally, we discuss how electronic laboratory notebooks fit into the broader context of research data management. This article is not a product review; it provides a framework for both the initial consideration of an electronic laboratory notebook and the evaluation of specific software packages.
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Affiliation(s)
- Stuart G Higgins
- Department of Materials, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
- Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Akemi A Nogiwa-Valdez
- Department of Materials, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
- Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Molly M Stevens
- Department of Materials, Imperial College London, London, UK.
- Department of Bioengineering, Imperial College London, London, UK.
- Institute of Biomedical Engineering, Imperial College London, London, UK.
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Barriers to Full Participation in the Open Science Life Cycle among Early Career Researchers. DATA SCIENCE JOURNAL 2022. [DOI: 10.5334/dsj-2022-002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Brock TCM, Elliott KC, Gladbach A, Moermond C, Romeis J, Seiler T, Solomon K, Peter Dohmen G. Open Science in regulatory environmental risk assessment. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2021; 17:1229-1242. [PMID: 33913617 PMCID: PMC8596791 DOI: 10.1002/ieam.4433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/22/2021] [Accepted: 04/16/2021] [Indexed: 05/14/2023]
Abstract
A possible way to alleviate the public skepticism toward regulatory science is to increase transparency by making all data and value judgments used in regulatory decision making accessible for public interpretation, ideally early on in the process, and following the concepts of Open Science. This paper discusses the opportunities and challenges in strengthening Open Science initiatives in regulatory environmental risk assessment (ERA). In this discussion paper, we argue that the benefits associated with Open Science in regulatory ERA far outweigh its perceived risks. All stakeholders involved in regulatory ERA (e.g., governmental regulatory authorities, private sector, academia, and nongovernmental organizations), as well as professional organizations like the Society of Environmental Toxicology and Chemistry, can play a key role in supporting the Open Science initiative, by promoting the use of recommended reporting criteria for reliability and relevance of data and tools used in ERA, and by developing a communication strategy for both professionals and nonprofessionals to transparently explain the socioeconomic value judgments and scientific principles underlying regulatory ERA. Integr Environ Assess Manag 2021;17:1229-1242. © 2021 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
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Affiliation(s)
| | - Kevin C. Elliott
- Department of Fisheries and WildlifeLyman Briggs College Department of PhilosophyMichigan State UniversityEast LansingMichiganUSA
- Department of PhilosophyLyman Briggs CollegeMichigan State UniversityEast LansingMichiganUSA
| | | | - Caroline Moermond
- National Institute for Public Health and the Environment (RIVM)UtrechtThe Netherlands
| | - Jörg Romeis
- Research Division Agroecology and EnvironmentAgroscopeZurichSwitzerland
| | - Thomas‐Benjamin Seiler
- Hygiene‐Institut des RuhrgebietsGelsenkirchenGermany
- Institute for Environmental ResearchRWTH Aachen UniversityAachenGermany
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Hart K, An S, Edwards AM, Mahadevan R, Master ER, Edwards EA. Could open science stimulate industry partnerships in
chemical engineering
university research? CAN J CHEM ENG 2021. [DOI: 10.1002/cjce.24077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kirsten Hart
- BioZone & Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario Canada
- University of Toronto Faculty of Law Toronto Ontario Canada
| | - Sung An
- BioZone & Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario Canada
- University of Toronto Faculty of Law Toronto Ontario Canada
| | - Aled M. Edwards
- Structural Genomics Consortium University of Toronto Toronto Ontario Canada
| | - Radhakrishnan Mahadevan
- BioZone & Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario Canada
| | - Emma R. Master
- BioZone & Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario Canada
| | - Elizabeth A. Edwards
- BioZone & Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario Canada
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Bafeta A, Bobe J, Clucas J, Gonsalves PP, Gruson-Daniel C, Hudson KL, Klein A, Krishnakumar A, McCollister-Slipp A, Lindner AB, Misevic D, Naslund JA, Nebeker C, Nikolaidis A, Pasquetto I, Sanchez G, Schapira M, Scheininger T, Schoeller F, Sólon Heinsfeld A, Taddei F. Ten simple rules for open human health research. PLoS Comput Biol 2020; 16:e1007846. [PMID: 32881878 PMCID: PMC7470254 DOI: 10.1371/journal.pcbi.1007846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Aïda Bafeta
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, Paris, France
| | - Jason Bobe
- Institute for Next Generation Healthcare, New York, New York, United States of America
| | - Jon Clucas
- MATTER Lab, Child Mind Institute, New York, New York, United States of America
| | | | - Célya Gruson-Daniel
- COSTECH, Université de Technologie de Compiègne, Compiègne, France; LabCMO, Université du Québec à Montréal, Université Laval, Montreal, Canada
| | - Kathy L. Hudson
- Hudson Works LLC, Washington, District of Columbia, United States of America
| | - Arno Klein
- MATTER Lab, Child Mind Institute, New York, New York, United States of America
| | - Anirudh Krishnakumar
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, Paris, France
| | | | - Ariel B. Lindner
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, Paris, France
| | - Dusan Misevic
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, Paris, France
| | - John A. Naslund
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Camille Nebeker
- Department of Family Medicine and Public Health, School of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Aki Nikolaidis
- Center for the Developing Brain, Child Mind Institute, New York, New York, United States of America
| | - Irene Pasquetto
- Harvard Kennedy School, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Matthieu Schapira
- Structural Genomics Consortium and Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada
| | - Tohar Scheininger
- Healthy Brain Network, Child Mind Institute, New York, New York, United States of America
| | - Félix Schoeller
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, Paris, France
| | - Anibal Sólon Heinsfeld
- Center for the Developing Brain, Child Mind Institute, New York, New York, United States of America
| | - François Taddei
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, Paris, France
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Abstract
Preregistration of study protocols and, in particular, Registered Reports are novel publishing formats that are currently gaining substantial traction. Besides rating the research question and soundness of methodology over outstanding significance of the results, they can help with antagonizing inadequate statistical power, selective reporting of results, undisclosed analytic flexibility, as well as publication bias. Preregistration works well when a clear hypothesis, primary outcome, and mode of analysis can be formulated. But is it also applicable and useful in discovery research, which develops theories and hypotheses, measurement techniques, and generates evidence that justifies further research? I will argue that only slight modifications are needed to harness the potential of preregistration and make exploratory research more trustworthy and useful.
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Affiliation(s)
- Ulrich Dirnagl
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
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Abstract
Six to swear by! Society needs effective and affordable medicines. We currently have at our disposal essentially one system to discover and develop drugs, and there are many areas where this system struggles to deliver, for example to combat antimicrobial resistance, or tropical diseases, or dementia. It is sensible to cultivate alternative, competing approaches to drug discovery and development. A genuinely new alternative is to open up the entire research cycle, abandoning secrecy altogether. This "open source" approach has now been trialed and the lessons learned distilled to six laws of operation that help to clarify working practices. This article examines and explains those laws, which can be adopted by anyone wishing to create medicines using an inclusive, public process.
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Affiliation(s)
- Matthew H Todd
- School of Pharmacy, University College London, 29-39 Brunswick Square, WC1N 1AX, London, UK
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