RDA COVID-19 Guidelines and Recommendations

23
Apr
2020

RDA COVID-19 Guidelines and Recommendations

By Hilary Hanahoe


                                                                                                                                                                                                                                                                 

            

RDA COVID-19 Working Group

            

Group Co-chairs: Juan Bicarregui, Anne Cambon-Thomsen, Ingrid Dillo, Natalie HarrowerSarah Jones, Mark Leggott, Priyanka Pillai

Subgroup Moderators

Clinical: Sergio BoniniDawei LinAndrea Jackson-Dipina, Christian Ohmann

Community Participation:  Timea BiroKheeran DharmawardenaEva MéndezDaniel MietchenSusanna SansoneJoanne Stocks

Epidemiology:  Claire AustinGabriel Turinici

Indigenous Data: RDA International Indigenous Data Sovereignty Interest Group 

Legal and Ethical: Alexander BernierJohn Brian Pickering

Omics: Natalie MeyersRob Hooft

Social Sciences: Iryna KuchmaAmy Pienta

Software: Michelle BarkerHugh ShanahanFotis Psomopoulos

Editorial team: Christoph Bahim, Alexandre BeaufaysIngrid Dillo, Natalie Harrower, Mark Leggott, Nicolas LoozenRobyn NicholsonPriyanka Pillai, Mary Uhlmansiek, Meghan Underwood, Bridget Walker
            

Recommendation title:  RDA COVID-19; recommendations and guidelines, 5th release (final draft) 28 May 2020

       

Authors: RDA COVID-19 Working Group and Subgroup Members

            

DOI: https://doi.org/10.15497/rda00046

            

Citation:  RDA COVID-19 Working Group. recommendations and guidelines. Research Data Alliance. DOI: https://doi.org/10.15497/rda00046

Note: The overacrhing COVID-19 Working group includes the specific working group members, events, posts, wiki and documents can be viewed here:

  1. Clinical

  2. Community Participation

  3. Epidemiology

  4. Indigenous Data

  5. Legal and Ethical

  6. Omics

  7. Social Sciences

  8. Software

Disclaimer: The views and opinions expressed in this document are those of the individuals identified, and do not necessarily reflect the official policy or position of their respective employers, or of any government agency or organisation.

 

Context:

During a pandemic, data combined with the right context and meaning can be transformed into knowledge for informing public health responses. Timely and accurate collection, reporting and sharing of data with the research community, public health practitioners, clinicians and policy makers will inform assessment of the likely impact of a pandemic to implement efficient and effective response strategies.

Public health emergencies clearly demonstrate the challenges associated with rapid collection, sharing and dissemination of data and research findings to inform response. There is global capacity to implement systems to share data during a pandemic, yet the timeliness of accessing data and harmonisation across information systems are currently major roadblocks. The World Health Organisation’s (WHO) statement on data sharing during public health emergencies clearly summarises the need for timely sharing of preliminary results and research data. On 28 May 2020, the G7 Science and Technology Ministers’ Declaration on COVID-19 was issued, which calls for government-sponsored COVID-19 epidemiological and related research results, data, and information to be accessible to the public to the greatest extent possible.There is also a strong support for recognising open research data as a key component of pandemic preparedness and response, evidenced by the 117 cross-sectoral signatories to the Wellcome Trust statement on 31st January 2020, and the further agreement by 30 leading publishers on immediate open access to COVID-19 publications and underlying data. 

Objectives:

The objectives of the RDA COVID-19 Working Group (CWG) focusing on essential Clinical, Community Participation, Epidemiology, Indigenous Data, Legal & Ethical, Omics, and Social Sciences, and Software are:

  1. to clearly define detailed guidelines on data sharing under the present COVID-19 circumstances to help stakeholders follow best practices to maximize the efficiency of their work, and to act as a blueprint for future emergencies;
  2. to develop guidelines for policymakers to maximise timely, quality data sharing and appropriate responses in such health emergencies;
  3. to address the interests of researchers, policy makers, funders, publishers, and providers of data sharing infrastructures.

5th Release - Final Draft for public comment:

The RDA COVID-19 Working Group (CWG) members bring various expertise to develop a body of work that comprises how data from multiple disciplines inform response to a pandemic combined with guidelines and recommendations on data sharing under the present COVID-19 circumstances. The work has been divided into four research areas with four cross cutting themes, as a way to focus the conversations, and provide an initial set of guidelines in a tight timeframe. The detailed guidelines in this body of work is aimed to help stakeholders follow best practices to maximise the efficiency of their work, and to act as a blueprint for future emergencies. The recommendations in the document are aimed at helping policymakers and funders to maximise timely, quality data sharing and appropriate responses in such health emergencies. 

The CWG is addressing the development of such detailed guidelines on the deposit of different data sources in any common data hub or platform. The guidelines aim at developing a system for data sharing in public health emergencies that supports scientific research and policy making, including an overarching framework, common tools and processes, and principles that can be embedded in research practice. The guidelines contained herein  address general aspects that data should adhere to, for example the FAIR principles (that research outputs should be Findable, Accessible, Interoperable, and Reusable), or  the adoption of research domain community standards. 

These detailed guidelines are supplemented with higher level recommendations aimed at the other stakeholder groups who need to work together with the researchers and data stewards to realise the timely and open sharing of research data as a key component of pandemic preparedness and response.

The work has been divided into four research areas with four cross-cutting themes, as a way to focus the conversations, and provide an initial set of guidelines in a tight timeframe. 

The RDA COVID-19 WG was initiated after a conversation between the RDA and the European Commission. The first meeting of the CWG to determine the work was held in March. As of May, the CWG counted over 440 members, evenly spread across the different sub-groups. This effort also reflects the work of a host of other RDA Working Groups, as well as external stakeholder organisations, that has developed over a number of years. 

The CWG and the sub-groups operate according to the RDA guiding principles of Openness, Consensus, Balance, Harmonisation, Community-driven, Non-profit and technology-neutral and are open to all.

The 5th release (final draft) starts in Section 2 with an overview of foundational, overarching elements that emerged across the different research areas. These recommendations touch upon a number of well-known topics in research data sharing and align to the statements made by many organisations and governance bodies, including but not limited to, the WHO, the G7 Science and Technology Ministers, the publishing industry and Wellcome Trust.In Sections 3 to 6 the focus is on the COVID-19 related research areas. Each section starts with a description of the area and the focus and scope of the work done, followed by the actual recommendations and guidelines. In sections 7 to 10 this same structure is used for the four cross-cutting themes. The document contains an extended glossary of terms to support the reader (Section 11), an overview of useful additional resources (Section 12) and a list of references (Section 13). Section 14 lists the contributors to this work.

Timing and Future Releases:

This is the fifth and final draft of the Recommendations and Guidelines from the RDA COVID-19 working group, and is open for public comment until 8th of June 2020. Following the open period, feedback will be considered and then the WG will seek endorsement of the document from the RDA governance bodies prior to final publication.

More information and insights on the plans for those releases, as well as highlights from the sub-groups are given during the informative webinars – see COVID-19 WG Events page for details and to access previous recordings and presentations.

Request for Comments:

In the spirit of the RDA community and its open process, your feedback on the content of the releases, the scope, the direction, are vital for all involved to shape and focus the document and the sections to be a useful and meaningful tool.

A request from the editorial team: please indicate the section of the document or the indicator that your comment is about, and, if possible, also include a suggestion for improvement. Many thanks!

Output Status: 
Recommendations with RDA Endorsement in Process
Review period start: 
Friday, 24 April, 2020 to Monday, 8 June, 2020
Group content visibility: 
Public - accessible to all site users
Primary Domain/Field of Expertise: 
Social Sciences, Medical and Health Sciences, Humanities
Domain Agnostic: 
  • Patrick Dunn's picture

    Author: Patrick Dunn

    Date: 28 Apr, 2020

    What are the thoughts on the use of ISARIC-WHO Case Report Forms (CRFs) to collect data on individuals presenting with suspected or confirmed COVID-19 as a way of encouraging a core set of clinical data for COVID-19 patients?

     https://isaric.tghn.org/covid-19-clinical-research-resources/

    Apologies if this is redundant.

    Cheers,

    Patrick Dunn

  • Abdelkrim Boujraf's picture

    Author: Abdelkrim Boujraf

    Date: 30 Apr, 2020

    To whom it may concern,

    I am a bit knowledgable about software manufacturing;

     

    The recommendations are a source of useful information for IT Solutions Architects who want to implement the IT solutions supporting the five subgroups.

     

    Here are some challenges to ensure a smooth implementation of such IT Solutions: 

     

    • the explosion of software developed by individuals annihilates the support that public administration may provide in the mid-to-long term. Software engineers develop hundreds of dashboards, offering a minimal amount of added value. See a short list of dashboards (see 1)

     

    • the lack of awareness of the RD-Alliance activities by the Software industry, an industry that should profit from RDA' best practices

     

    • Each sub-group should provide a link to documentation describing their needs (for dummies). For example, the OMICS group did a great job describing the data models the researcher should use to store its data from cell and molecular biology; is it possible to explain in which context they use those data? (or is it out of scope?)

     

    • Do the sub-groups plan to build a tool or website that the community may use daily as a checklist? I started mine :-) (See 2)

     

     

    GREAT JOB!

    Abdelkrim Boujraf

     

     

    Links

    (1) https://data-visualization.readthedocs.io/en/latest/dataviz/dashboards.html

     

    (2) https://data-visualization.readthedocs.io/en/latest/dataviz/rda_covid-19...
     

  • Hugh Shanahan's picture

    Author: Hugh Shanahan

    Date: 03 Jun, 2020

    Hi - apologies for not getting to this. 

    I agree that Industry could benefit more from the outputs of the RDA (though there is some contact through specific industries such as Pharma).

    The scope of the report is for researchers, policy makers and publishers and hence to keep in scope we've not provided an introductory guide to the research topics themselves (as it is the document is 120 pages long). 

    There will be a decision tree to aid the above which I think is similar to what you're suggesting. 

    Thanks again

    Hugh

     

  • Mogens Thomsen's picture

    Author: Mogens Thomsen

    Date: 05 May, 2020

    As a member of the COVID-19 clinical subgroup  I have followed the webinars that were very informative and I  have had a look at the 2nd release of Recommendations and guidelines. The document looks promising.

    I have a few suggestions :

    4.2.4             first line

    it is critical to spend limited time and resources on reliable data sources …  I propose :

    it is important to concentrate the efforts on scrutinizing reliable data sources …

    4.3

    The list of additional working documents & links might be divided into references to articles and static web pages (item 4,6,7,8) and web sites with resources that are updated continuously.

    For the other sections of the document I would also prefer that additional working documents and links and also the references were separated as mentioned above.

    It is important that ISO standards are respected and in that context it should be avoided to have tables and figures with dates that do not follow the rules (e.g. 4/5 is the 5 April in US English and 4 May in UK English)

    Finally, it is a good idea to have two new overarching subgroups. However, for the legal and ethical guidelines there is some redundancy with some parts of the chapter 8.2.4 in the Social Sciences subgroup. But I am sure that this will be worked out.

    I look forward to see the 3rd release of the Guidelines.

    Best regards

    Mogens Thomsen

  • Nora Dörrenbächer's picture

    Author: Nora Dörrenbächer

    Date: 06 May, 2020

    Dear all,

    the German Data Forum (RatSWD) is an advisory council to the German federal government for the research data infrastructure of the social, behavioural and economic sciences, connecting a network of currently 34 accredited Research Data Centres. We are an organisational member of RDA since 2015. Currently, we are also working on ways to provide researchers with guidelines on how to manage their data when researching the impact of Covid 19 on social issues (see here) – with a focus on research in German speaking countries. Therefore, we are highly excited about the initiative of the RDA Covid 19 working group to establish standards for data sharing and highly welcome the initiative. We would like to add the following suggestion to the 2nd release document:

     

    8.2.2 Documentation, Standards, and Data Quality:

    (addition) Ensuring data quality

    In case of data collection using smartphone apps and other sensors:

    • note that most sensors are created as consumer products and their data quality does not meet the scientific demands to reliability and validity per se. Therefore, critically assess and document the data collection process, measurement accuracy, and the validity of the inferences
    • think about replicability of research – thorough research data management keeping in mind archiving raw data, software as well as hardware details and their versions as well as used code.
    • think about contractual restrictions, data protection and research ethics: researcher should make sure they have the rights to use sensor-based data or log files, the used format of informed consent should be – if applicable – confirmed by the actors or councils in charge. The consent forms should cover the archiving and reuse of data; 
    • For specific recommendations see German Data Forum (RatSWD) (2020): Data collection using new information technology: Recommendations on data quality, -management, research ethics, and data protection Output 6 (6). https://doi.org/10.17620/02671.47. Berlin (soon available in English)

    8.2.3. Storage and Backup:

    Highlight that much social science data is sensitive personal data. Before sharing and storing the data anonymisation and/or pseudonymisation must be implemented.

    8.2.4 Legal and Ethical Requirements:

    Specify point. 2

    Researchers have a responsibility for ensuring research participants understand that there may be a risk of re-identification when data are shared. Generally, researchers should take all possible measures to reduce the risk of re-identification. These attempts should be documented.

     

    Add a section

    8.2.6. Ensuing access to data in times of the Corona pandemic

    Formally anonymized microdata from official statistics are a central basis of numerous empirical research projects. Often, this data can only be used by researchers in a fixed location at guest workstations or via remote execution (i.e. generally without viewing and browsing data or results on the screen). In the current Corona pandemic, guest workstations are hardly usable and researchers have to work in their home office. Consequently, they no longer have access to important data.

    Recommendation:

    • Establishing remote access to individual data from the researcher's workplace makes research processes more flexible. Expensive and time-consuming business trips are no longer necessary while securing still high levels of data protection. Role models already exist in a number of European statistical offices and German research institutions (for more information see: https://www.ratswd.de/en/publication/output-series/2855).

  • Dawei Lin's picture

    Author: Dawei Lin

    Date: 06 May, 2020

    7.2.1 Recommendations for virus genomics data Repositories

    For assembled and annotated genomes we suggest deposition in one or more of these archives: NCBI GenBank, DDBJ Annotated/Assembled sequences, European Nucleotide Archive (ENA) Assembled/Annotated sequences, and/or NCBI Virus.

     

    The 'and/or NCBI Virus' should be removed. NCBI Virus is a custom view of GenBank and RefSeq data, plus added analysis tools.

     

    Under 7.2.2 -  What is listed for 'Cell lines/Animals' is surprising as they are all gene expression resources not sample metadata resources.  I would consider listing INSDC BioSample resources there instead.

    Kim D. Pruitt, Ph.D

    Chief, Information Engineering Branch

    NCBI/NLM/NIH

     

     

  • Rob Hooft's picture

    Author: Rob Hooft

    Date: 14 May, 2020

    Dear Kim,

    Thank you very much for your review of our draft recommendation. We have taken your suggestions to heart and  now refer to NCBI Virus as a NCBI genbank subrecource. We have also made it more clear that submission to the genome-phenome and genome expression archives leads to creation of several data sets in multiple databases that are linked to each other.

    Rob Hooft, representing The Omics team
     

  • Peter Cornwell's picture

    Author: Peter Cornwell

    Date: 21 May, 2020

    There is duplication between statements made under the Community Participation and Data Sharing Section 4., and Data Sharing in Social Sciences 7. While restrictions about data sharing in SS are more specific and Section 7. might warrant independent clarification, 7.4.5 is currently fairly generic and also more comprehensive than the text at 4.4.3. The Epidemiology and Omics sections don't seem to have separate preservation discussions. The analysis preservation statements currently at the bottom of page 66 are valuable, if ambitious. As a quick fix maybe you would consider replacing 4.4.3 with the text at 7.4.5 ?

    The preservation advice is basically use repository technology if possible; preferably a "trustworthy digital repository committed to preservation"; even better a "disciplinary repository .. for maximum visibility". It is worth recalling that in 2019 DataCite r3d100011136 which represented a major output of the Gates Foundation project on malaria at https://www.vecnet.org/ (these links still probably don't go anywhere) became unavailable. It had to be redelivered from an unsupported Fedora version using donated funds because this was too unfashionable for mainstream funders. Hopefully we can protect COVID research data more effectively. Maybe you would also consider building a repository of COVID publications similar to the vecnet model, with the benefit of current outputs rather than having to gather material from previous decades. Automated treatment techniques pioneered by Plazi in biodiversity could then be applied to significantly increase accessibility.

  • Natalie Harrower's picture

    Author: Natalie Harrower

    Date: 03 Jun, 2020

    Dear Peter thank you for you comment. We have made substantial revisions in the latest release (5th/28th May) with an attempt to remove duplication. Please let us konw if you find any remaining issues on your points. Many thanks.

  • Laurence DELHAES's picture

    Author: Laurence DELHAES

    Date: 30 May, 2020

    Hi everyone 

    Great job ! 

    No specific comment for me. 

    Cheers

    Laurence

  • Natalie Harrower's picture

    Author: Natalie Harrower

    Date: 03 Jun, 2020

    On behalf of all the contributors, thank you, Laurence!

  • Manuela Teresa Raimondi's picture

    Author: Manuela Teresa ...

    Date: 03 Jun, 2020

    Dear RDA COVID-19 Working Group 2020,

    thanks for the huge work undertaken. May I suggest a further point, i.e. the promotion of "pre-clinical" data sharing as a cross-cutting theme transversal to many others including Clinical, Omics and Community.

    The decision on which therapeutic agents or vaccinal strategies to bring into clinics, should be dictated by standard-shared and data-shared scientific evidence. This evidence should be based on integrated results of existing in silico, in vitro and in vivo preclinical studies. To speed-up the development of drugs, the experimental studies, in particular, should be based on the use of cutting-edge research tools instead of conventional tools that have a limited predictive capability. I have reviewed the updated set of research tools (in silico, in vitro and in vivo) already used in virology and vaccinology in the context of SARS-CoV-2: https://www.thno.org/v10p7034.htm. Sharing of pre-clinical data would speed-up the validation of these new tools, leading to an update of the current preclinical testing standards used by the pharmaceutical industry. This would improve the efficiency and effectiveness of the whole drug development process in virology and vaccinology, and many other pharmaceutical sectors as well.

    My best regards, Manuela T. Raimondi (www.nichoid.polimi.it)

    ATTACHMENT: 
    AttachmentSize
    PDF icon v10p7034.pdf2.22 MB

  • Natalie Harrower's picture

    Author: Natalie Harrower

    Date: 03 Jun, 2020

    Dear Manuela, thank you for your comments. I have raised your point with the WG for discussion.

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