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RDA COVID-19 Working Group Recommendations and Guidelines 4Th Release 15 May 2020

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RDA COVID-19 Working Group Recommendations and Guidelines 4Th Release 15 May 2020 RDA COVID-19 Working Group Recommendations and Guidelines 4th Release 15 May 2020 RDA Recommendation (4th Release - 15 May 2020) Produced by: RDA COVID-19 Working Group, 2020 Document Metadata Identifier DOI: 10.15497/RDA00046 Title RDA COVID-19; recommendations and guidelines, 4th release 15 May 2020 Description This is the fourth draft of the “overarching” RDA COVID-19 Guidelines document, and is intended to provide an update on the progress of the WG, as well as a focus on high-level recommendations that run across all 5 sub-groups in this initial effort, as well as the cross-cutting themes of Research Software and Legal and Ethical . Date Issued 2020-05-15 Version Draft guidelines and recommendations; fourth release, 15 May 2020, version for public review Contributors RDA COVID-19 Working Group This work was developed as part of the Research Data Alliance (RDA) ‘WG’ entitled ‘RDA-COVID19,’ ‘RDA-COVID19-Clinical,’ ‘RDA-COVID19- Community-participation,' ‘RDA-COVID19-Epidemiology,’ ‘RDA- COVID19-Legal-Ethical,’ ‘RDA-COVID19-Omics,’ ‘RDA-COVID19-Social- Sciences,’ ‘RDA-COVID19-Software,’ and we acknowledge the support provided by the RDA community and structure. Licence This work is licensed under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication. Disclaimer The views and opinions expressed in this document are those of the individuals identified (below), and do not necessarily reflect the official policy or position of their respective employers, or of any government agency or organization. RDA COVID-19; recommendations and guidelines, 4th release 15 May 2020 1 Group Co-chairs: Juan Bicarregui, Anne Cambon-Thomsen, Ingrid Dillo, Natalie Harrower, Sarah Jones, Mark Leggott, Priyanka Pillai Subgroup Clinical: Sergio Bonini, Dawei Lin, Andrea Jackson-Dipina, Christian Moderators: Ohmann Community Participation: Timea Biro, Kheeran Dharmawardena, Eva Méndez, Daniel Mietchen, Susanna Sansone, Joanne Stocks Epidemiology: Claire Austin, Gabriel Turinici Legal and Ethical: Alexander Bernier, John Brian Pickering Omics: Natalie Meyers, Rob Hooft Social Sciences: Iryna Kuchma, Amy Pienta Software: Michelle Barker, Hugh Shanahan, Fotis Psomopoulos Editorial team: Christophe Bahim, Alexandre Beaufays, Ingrid Dillo, Natalie Harrower, Mark Leggott, Nicolas Loozen, Priyanka Pillai, Mary Uhlmansiek, Meghan Underwood, Bridget Walker History of the discussions in the Working Groups that led to this document can be viewed in the comments made in the associated subgroup documents. The views and opinions expressed in this document are those of the individuals identified (below), and do not necessarily reflect the official policy or position of their respective employers, or of any government agency or organization. RDA COVID-19; recommendations and guidelines, 4th release 15 May 2020 2 Table of Contents Table of Figures 6 1. Objectives and Use of This Document 8 2. Foundational Recommendations 10 2.1 Challenges 10 2.2 Recommendations 11 3. Data Sharing in Clinical Medicine 13 3.1 Focus and Description 13 3.2 Scope 13 3.3 Policy Recommendations 13 3.3.1 Sharing Clinical Data 13 3.3.2 Trustworthy Sources of Clinical Data 14 3.4 Guidelines 17 3.4.1 Clinical Trials on COVID-19 17 3.4.2 Other Types of Data 18 4. Community Participation and Data Sharing 20 4.1 Focus and Description 20 4.2 Scope 21 4.3 Policy Recommendations 22 4.3.1 Data Collection 22 4.3.2 Data Quality and Documentation 23 4.3.3 Legal and Ethical Aspects 23 4.3.4 Software Development 23 4.4 Guidelines 23 4.4.1 Data Collection 24 4.4.2 Data Quality and Documentation 24 4.4.3 Data Storage and Long-Term Preservation 24 4.4.4 Transparency and Community Participation 25 5. Data Sharing in Epidemiology 26 5.1 Focus and Description 26 5.2 Scope 26 5.3 Recommendations 28 5.3.1 Policy 28 5.3.2 Information Technology And Data Management Infrastructure 28 RDA COVID-19; recommendations and guidelines, 4th release 15 May 2020 3 5.3.3 Analysis and Modeling 28 5.3.4 Surveillance Data 28 5.3.5 Global preparation, detection, and response 28 5.3.6 Interoperability and Data Exchange 28 5.4 Guidelines 29 5.4.1 Policy 29 5.4.2 Information Technology and Data Management Infrastructure 29 5.4.3 Analysis and Modeling 30 5.4.4 Surveillance Data 30 5.4.6 Interoperability and Data Exchange 34 5.4.6.1 COVID-19 Questionnaire Initiatives 34 5.4.6.2 COVID-19 Question Bank 40 5.4.6.3 COVID-19 Use Case for Common Data Models 42 5.4.6.4 Anonymization and Pseudonymization 44 6. Data Sharing in Omics Practices 47 6.1 Focus and Description 47 6.2 Scope 47 6.3 Policy Recommendations 47 6.3.1 Researchers Producing Data 47 6.3.2 Funders 48 6.3.3 Publishers 49 6.3.4 Policymakers 49 6.3.5 Researchers 49 6.3.6 Providers of Data Sharing Infrastructures 49 6.4 Guidelines 50 6.4.1 Recommendations for Virus Genomics Data 50 6.4.1.1 Repositories 50 6.4.1.2 Data and Metadata Standards 50 6.4.2 Recommendations for Host Genomics Data 51 6.4.2.1 Generic Recommendations 52 6.4.2.2 Repositories 52 6.4.2.3 Data and Metadata Standards 53 6.4.3 Recommendations for Structural Data 54 6.4.3.1 Repositories 54 RDA COVID-19; recommendations and guidelines, 4th release 15 May 2020 4 6.4.3.2 Locating Existing Data 54 6.4.3.3 Data and Metadata Standards 54 6.4.4 Recommendations for Proteomics 56 6.4.4.1 Repositories 56 6.4.4.2 Data and Metadata Standards 57 6.4.5 Recommendations for Metabolomics 57 6.4.5.1 Repositories 57 6.4.5.2 Data and Metadata Standards 57 6.4.6 Recommendations for Lipidomics 58 6.4.6.1 Generic Recommendations for Researchers 58 6.4.6.2 Repositories 58 6.4.6.3 Data and Metadata Standards 58 7. Data Sharing in Social Sciences 60 7.1 Focus and Description 60 7.2 Scope 60 7.3 Policy Recommendations 61 7.4 Guidelines 62 7.4.1 Data Management Responsibilities and Resources 62 7.4.2 Documentation, Standards, and Data Quality 63 7.4.3 Storage and Backup 64 7.4.4 Legal and Ethical Requirements 64 7.4.5 Data Sharing and Long-term Preservation 65 8. Research Software and Data Sharing 67 8.1 Focus and Description 67 8.2 Scope 67 8.3 Policy Recommendations 67 8.4 Guidelines for Publishers 70 8.5 Guidelines for Researchers 71 9. Legal and Ethical Compliance 73 9.1 Focus and Description 73 9.2 Scope 73 9.3 Policy Recommendations 74 9.3.1 Initial Recommendations 74 9.3.2 Relevant Policy and Non-Policy Statements 75 RDA COVID-19; recommendations and guidelines, 4th release 15 May 2020 5 9.4 Guidelines 75 9.4.1 Cross-Cutting Principles 75 9.4.2 Hierarchy of Obligations 76 9.4.3 Seeking Guidance 77 9.4.4 Anonymisation 78 9.4.5 Consent 80 9.4.6 The 5 Safes Model: Safe People, Safe Projects, Safe Settings, Safe Outputs, Safe Data 81 10. Additional Working Documents 83 11. References 86 12. Contributors 107 Table of Figures Figure 1...................................................................................................................................... 8 Figure 2.....................................................................................................................................27 Figure 3. ...................................................................................................................................32 Figure 4.....................................................................................................................................34 Figure 5.....................................................................................................................................41 Figure 6.....................................................................................................................................45 Figure 7.....................................................................................................................................45 Figure 8.....................................................................................................................................46 Table of Tables Table 1 Questionnaire instruments: Reference studies. Development of such initiatives is a very active and rapidly changing area at the present time during the COVID-9 pandemic. Contributed by Dr. Carsten Schmidt, Dr Jay Greenfield, Dr. Stefen Sauermann, and Dr. Chifundo Kanjala, developed from discussions held during RDA-COVID19-Epidemiology Work Group meetings .35 Table 2 Questionnaire instruments - Resources. Development of such initiatives is a very active and rapidly changing area at the present time during the COVID-9 pandemic. .........................40 RDA COVID-19; recommendations and guidelines, 4th release 15 May 2020 6 0. Log Changes Document Changes Date RDA COVID-19; First draft of document released for comments and feedback 24 April 2020 recommendations and guidelines, 1st release 24 April 2020 RDA COVID-19; Section 3 - Foundational Principles/Recommendations - 1 May 2020 recommendations and modifications guidelines, 2nd release 1 Section 4 - Clinical - updated May 2020 Section 6 - Epidemiology - revised Section 8 - Omics - revised Section 9 - Overarching Research Software Guidelines - new sub- section 9.3 initial guidelines for policy makers included Section 10 - Overarching Legal and Ethical Guidelines added Incorporation of feedback received via Requests for Comments (RfC) process and directly to Co-chairs, moderators and editorial team RDA COVID-19; Section 3 - Foundational Principles/Recommendations - updates 8 May 2020 recommendations and and additional content guidelines, 3rd release 8 Section 4 - Clinical - Revisions to sections 4.2.3, 4.2.4, and 4.3. May 2020 Newly added section 4.2.5 Section 5 - Community Participation: Use case section 5.2.2
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