Please note the final planned GREGoR website downtime in April:

  • Friday, April 19  at 5 pm PT to Monday April 22 at 8 am PT (63 hours)

During this time the GREGoR website will be down and users will be unable to log into the DCC's AnVIL management web app to link their AnVIL accounts. Please contact the DCC at gregorconsortium@uw.edu if you have questions or need help during the downtime.

GREGoR Consortium Publications Policy

Date Approved: September 16, 2022

Date of Last Update: March 7, 2024

Version: 1.4

Table of Contents

  1. Background
  2. Scope
  3. Policy
    1. Publication Types
    2. Notification and Comment Process
    3. Roles
    4. Authorship
    5. Acknowledgements
    6. Submitting Abstracts to Scientific Meetings
    7. Data Sharing
    8. Relevant NIH Policies
      1. Public Access Policy
      2. Communicating and Acknowledging Federal Funding
    9. Preprint Policy and Guidance
  4. Related Policies
  5. Change Log
  6. Appendix 1. Summary of policy and process by GREGoR Publication Type
  7. Appendix 2. Funding Acknowledgements
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Background

The publication policy established by the GREGoR Consortium is meant to (1) create transparency and foster collaboration within the Consortium, (2) encourage and facilitate timely circulation of GREGoR Consortium work products, (3) ensure appropriate use of Consortium data, (4) support adherence to authorship principles, (5) comply with the NIH Public Access Policy, and (6) maintain a complete, up-to-date list of GREGoR publications.

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Scope

This policy applies to any scientific work carried out by GREGoR members (core and partner) where GREGoR funding is used for participant recruitment, data generation, and/or data analysis. Consortium commentaries, perspectives, and “best practices” manuscripts are also within scope. See Appendix 1 for an overview of policy and process across different GREGoR publication types, each of which is in scope of this policy.

This policy does not apply to the following activities:

  • Publications or abstracts from non-GREGoR members
  • Publications or abstracts led by non-GREGoR members for which one or more GREGoR investigators provide consultation and input that does not use data or resources from GREGoR
  • Publications or abstracts from GREGoR members using samples collected via the prior Centers for Mendelian Genomics (CMG) program collaborator agreements, prior to GREGoR funding, unless the analysis is using resources and methods from GREGoR
    • Note while not in scope of the policy, guidance on acknowledgements language is provided below

Publications citing one or more GREGoR grants are expected to be within scope. Should there be uncertainty about whether the policy applies, investigators are encouraged to contact the GREGoR DCC or, if needed, the GREGoR Steering Committee.

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Policy

Publication Types

The publication notification and comment requirements and procedures in GREGoR differ by publication type. Publication type is defined by (1) which samples are used and (2) which group(s) are primarily performing the analyses. This leads to six publication types, labeled (A) - (F) (see Appendix 1). No publication type requires approval from the GREGoR Consortium, and there is no designated body to review submitted publication notification forms (i.e. no GREGoR Publications Committee).

Notification and Comment Process

Notification

Timely notification of GREGoR publications is important for creating transparency and maximizing opportunities for collaboration within the Consortium. Notification occurs when a lead author or designee submits a publication notification form via the internal GREGoR Consortium website, providing basic information such as topic/title, dataset(s) used, and Research Center(s) involved. Submitted publication notification forms are viewable by all logged-in members on the internal Consortium website.

  • For publication types B-F, the notification form is to be submitted at the manuscript concept stage.
  • For publication type A (collaborator-led analysis), the notification form is ideally submitted prior to publication; however, the notification form can still be submitted after publication to allow tracking of these manuscripts.

Comment

All GREGoR Consortium members (core and partner members) are welcome to comment on submitted publication notification forms. Comments are to be submitted in the two-week window following submission to the website.

  • For publication types C-F, the Contact PI (or their designee) from each Research Center will be notified directly (via email) when a new publication notification form is submitted. They are not required to comment or respond.

Status Updates

Submitting authors will receive auto-generated emails from the Consortium website every 6 months, prompting them to report to the DCC any major updates on their submitted publication notification forms. Major updates include pre-print available (provide DOI), published (provide PubMed ID), changes to key contacts, or archived/no longer moving forward. Authors may also proactively provide such updates to the DCC at any time.

Roles

Roles in the GREGoR publication processes are as follows:

Data Coordinating Center (DCC)

  • Maintains online systems for publication notification form submissions, comments from Consortium members, and direct notifications of Contact PIs (or their designee) for publication types C-F
  • Maintains current list of submitted publications and abstracts on internal Consortium website
  • Maintains public-facing list of published or pre-printed publications and abstracts on Consortium website
  • Maintains current list of banner authors on Consortium website

Submitting author

  • Submits publication notification form in a timely manner, according to expectations by publication type
  • Responds to requests for status updates, including providing DCC with a DOI (when pre-printed) or PubMed ID (when published)

Research Center PIs

  • Contact PIs (or their designee) receive direct notifications of newly-submitted publications to the website for publication types C-F
  • Determine who from their Center should be listed on the Consortium banner and communicate any updates to banner author members to the DCC

Steering Committee (SC)

  • Adjudicates publication-related conflicts
    • Publication-related concerns or potential conflicts can be raised to the SC co-chairs and/or the DCC, who will triage as needed.

Consortium members

  • GREGoR Consortium members (core and partner) are invited (but not required) to submit comments on publication notification forms in the two-week window following submission to the GREGoR website

Authorship

Facilitating cross-Consortium collaboration is a key element of the GREGoR Consortium and this publications policy. Authorship should be discussed early in the process (e.g. at manuscript concept stage) to enable substantive contribution and fairness in representation. Principles of authorship in GREGoR include:

  • Inclusivity
  • Providing opportunities for trainees and early stage investigators
  • Recognition of sample recruitment and phenotyping
  • Adherence to standard authorship criteria (see ICMJE standards)

Banner authorship

For manuscripts utilizing cross-GREGoR Consortium data and/or other cross-Consortium contributions (publication types D-F), banner authorship is required to acknowledge the efforts of the Consortium. A list of the members of the banner are maintained by the DCC on the Consortium website. Center PIs decide which core members from their group are on the Consortium banner and communicate that (along with any updates or changes) to the DCC. We encourage inclusion of core members who are contributing to GREGoR. Partner members are not eligible for inclusion on the Consortium banner.

For manuscripts deriving from GREGoR Working Groups, it is at the discretion of the WG to determine if a banner authorship for the WG is appropriate. If appropriate, please refer to the GREGoR website for the current list of WG members.

Acknowledgements

All relevant papers should include a statement citing the NIH grant support for the work, listing the appropriate grant number(s) and acknowledging the GREGoR Consortium (see Appendix 2).

Submitting Abstracts to Scientific Meetings

Abstracts do not require notification to the GREGoR Consortium before submission to a conference; however, co-authors on the abstract should be notified with at least 48 hours notice. While not required, submission of an abstract to the GREGoR website prior to the conference is encouraged. A list of all abstracts submitted to the DCC will be maintained on the website by the DCC. The same authorship considerations apply to abstracts as to manuscripts.

Data Sharing

All authors should ensure that their analysis is consistent with all conditions of the NIH Genomic Data Sharing Policy and related GREGoR Consortium policies (see Related Policies below). Points to consider for sharing include variant level information with ClinVar (Azzariti et al. 2018), Institutional Review Board (IRB)-approved protocols, informed consent forms signed by Research Participants, HIPAA, and Title XIII of the American Recovery and Reinvestment Act of 2009.

Relevant NIH Policies

Public Access Policy

Please note, all manuscripts developed by or in association with the GREGoR Consortium must be deposited in PubMed Central. This step is critical for ongoing NIH funding, and authors should be aware of this requirement prior to submitting any article to a journal. For more information on this process, please visit the NIH Public Access Policy.

Communicating and Acknowledging Federal Funding

The NIH provides guidance to awardees on when and how to acknowledge grant funding. Please refer to this guidance to inform which publications should cite your GREGoR grant (see also Appendix 2 for sample Acknowledgements language). Note that publications citing GREGoR grants are expected to be within scope of this Publications Policy, and therefore submitted to the Consortium website according to the procedures herein. 

  • Note: it can be helpful for transparency purposes to include what the grant funding was specifically used for (i.e. sequencing, analysis, advisory role only)

Correct citation practices also facilitate tracking in resources such as PubMed, PubMed Central, RePORTER, and NCBI My Bibliography. Note GREGoR investigators are responsible for maintaining publication records and linkages in these NIH resources, in addition to submitting records for the GREGoR website. 

Preprint Policy and Guidance

The GREGoR Consortium strongly encourages submission of all publications to a preprint server in advance of submission for publication to ensure timely access to scientific work.

  • For publication types B-F (see Appendix 1), preprint submission is required at time of submission for publication to a journal.
    • If necessary, requests for exceptions can be made to the NHGRI program office
  • For publication type A (collaborator-led analysis), preprint submission is strongly encouraged at time of submission for publication to a journal.

Preprint Servers

  • Two primary preprint servers exist for biomedical literature, bioRxiv and medRxiv. Any article that includes claims about disease causality should go to medRxiv and not bioRxiv.
  • Please note, because the goal of preprint servers is to have access to the results of scientific investigations that can take many months to years to publish, these preprint servers reject papers that are solely based on opinions. They receive a large number of submissions daily and review them to ensure they are research studies, not opinion papers. To do this, they look for data and methods with a focus on whether the study has a methodology that could allow it to be replicated.
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Change Log

  • V1.4 - Clarify relationship of Consortium Policy to required NIH reporting and grant citation practices. Clarify that publications citing one or more GREGoR grants are expected to be within scope.
  • V1.3 - Clarifying that that core (rather than partner) members are eligible for the Consortium banner author
  • V1.2 – Minor update to Appendix 1 figure
  • V1.1 - Minor clarifications made during course of SC review, (e.g. scope and timing of abstract submission, mechanism to raise publication-related conflicts)
  • V1.0 - Initial Policy distributed for SC vote
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Appendix 1. Summary of policy and process by GREGoR Publication Type

Summary table of Publication Types, Policies, and Processes

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Appendix 2. Funding Acknowledgements

  1. Papers that use data from the entire GREGoR Consortium or collaborate with the Consortium:

    The GREGoR Consortium is funded by the National Human Genome Research Institute of the National Institutes of Health, through the following grants: U01HG011758, U01HG011755, U01HG011745, U01HG011762, U01HG011744, and U24HG011746. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

    Optionally, the acknowledgements statement may also list GREGoR Research Centers and Principal Investigators; see website for current list.
  2. Papers specific to certain GREGoR Consortium grants and only use a subset of GREGoR data. Note this template can also be used for papers with CMG-funded data and samples:

    This publication was supported [in part] by the National Human Genome Research Institute of the National Institutes of Health through the following grants, as part of GREGoR Consortium: [add specific GREGoR grant number(s)*]; and [add non-GREGoR grant number(s)]. The content is solely the responsibility of the author and does not necessarily represent the official views of the National Institutes of Health.

    *GREGoR grant numbers are listed on the Center-specific pages linked from https://gregorconsortium.org/members/centers.
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