Publication Policy SenNet Consortium*
Approved by the SenNet Consortium Steering Committee July 20, 2022
This document provides publication policy for the SenNet Consortium (or ‘SenNet’) that has been agreed to by the entire SenNet through ratification by the SenNet Steering Committee. It covers the goals and guidelines that apply to authorship, acknowledgements, metrics tracking etc. related to the dissemination of SenNet supported products. It covers all products of the SenNet consortium that convey information outside the members of the Consortium including Journal Articles; Preprints; Conference/Meeting Abstracts/Proceedings/Presentations; White Papers; Workshops; Software and Data Releases; Protocols, and Policies.
SenNet, like many other NIH programs, will follow “rapid data release” policies to the community. Working papers and/or white papers generated by the SenNet consortium will be used to inform the research community, and we will accept feedback on all aspects of the data-release process. It is expected that SenNet data will be released after “data verification”, which is defined as assessing the usability of the data. That is, the data have sufficient quality to support its use in follow-up experiments. The working/white papers will provide additional and assay-specific details at the time of data release.
The goals of this policy are to:
- Encourage collaborative work within SenNet.
- Promote transparency and fairness within SenNet (see authorship, stable identifiers, acknowledgment below) and with the wider research community.
- Guide and encourage communication within SenNet regarding plans for publications.
- Promote the rapid dissemination of research products, through the use of publicly available and commonly used preprint servers for publications, websites for protocols, software and presentations, and databases for datasets.
- Make SenNet products fully adhere to FAIR (Findability, Accessibility, Interoperability, Reusability https://en.wikipedia.org/wiki/FAIR_data) principles by using publicly available persistent identifiers for:
- authors (e.g., ORCID),
- data (e.g., DOI or SenNet universally unique identifiers [UUIDs]),
- experimental protocols (e.g., protocols.io ID),
- metadata ( e.g., identifiers.org, https://www.scicrunch.org/resources),
- software (e.g., https://registry.identifiers.org/registry/swh for Software Heritage persistent identifiers).
To balance the academic interests of the consortium members with the goals of this policy, producers are asked to publicly release their products within six months of generating them. This will provide time for the resource producers to have a protected opportunity to publish initial analyses of any data they have generated.
Guidelines on Authorship
It is expected that SenNet consortium members will follow the general guidelines prevalent in the research community regarding authorship as outlined by the Council of Science Editors White Paper on Publication Ethics (see Section 2.2 on ”Authorship and Authorship Responsibilities”).
Guidelines on Peer-Reviewed Publications by SenNet Consortium Members
- Standard Operating Procedures – Internal and External Sharing
- All experimental SOPs used in SenNet will be made available on protocols.io https://www.protocols.io/
- “Publication” refers to all products as defined in the first paragraph of this document, including journal articles and major national or international scientific presentations.
- Journals with Open Access publication options are preferred for all SenNet publications. Gold (made freely and immediately accessible by journal upon publication) or green (self-archiving) journals open access publication are acceptable. At a minimum, authors need to comply with the NIH Public Access policy (https://publicaccess.nih.gov/).
- The sharing / publication of data not officially released by SenNet is governed by the SenNet External Data Use Policy and must be disclosed to the SenNet Steering Committee Chairs. As outlined in the SenNet External Data Use Policy, the SenNet Steering Committee Chairs may seek the council of the full SenNet Steering Committee.
- Internal Manuscript and Major National/International Presentation tracking
- Planned manuscripts & presentations must be logged on a SenNet tracker for preview by SenNet Members.
- The SenNet tracker records must list planned publications by title, brief description, person point of contact, and stages of publication. This will be for internal use, password-protected, confidential communication only.
- To encourage collaboration and coordination, it is expected that all publications will be reported here well in advance, preferably as the idea is being formulated.
- The SenNet tracker will provide a time stamp for abstracts and manuscripts, while also providing an internal timeline of development.
- The SenNet tracker will be used to identify conflicts and collaborative opportunities in publication plans that will be reviewed by the SenNet Steering Committee on a regular basis.
- Mandatory submission of manuscripts to a preprint server such as bioRxiv, aRxiv, etc.
- Posting should be prior to or at the time of submission to a publication venue.
- If additional time is required after manuscript submission for preprint posting due to delays in securing intellectual property, the investigator may apply for an extension by contacting the SenNet Steering Committee Chairs.
- Preprints must be complete manuscripts in form suitable for publication.
- Citing of preprints, pending journal publication, is expected.
- Manuscript submission and preprint status (availability) should be announced at the SenNet Steering Committee meetings and/or via the SenNet Newsletter.
The overarching guiding principle for joint publications of SenNet is to exploit the rich expertise of the SenNet members by producing manuscripts that describe comprehensive, in-depth studies of human tissues at the cellular and molecular level driven by data sets generated by SenNet. Beyond these joint publications, members of SenNet are expected to rapidly disseminate manuscripts describing any insights, methods, procedures, or data sets that enable the broader community to make further progress in this field of research.
SenNet anticipates the following publication types:
- Flagship Papers
- Overall (consortium-wide)
- Organ-centric (SenNet-wide or organ-specific collaborations)
Flagship manuscripts will be coordinated across the whole SenNet with the goal of publishing a collection of open-access papers in a top-tier journal approximately every other year. The availability of preprints of these papers should coincide with a major data release. However, we will ensure that flagship manuscript publication does not cause a delay in data release. It will be the responsibility of the SenNet PIs to organize the content of the flagship papers and negotiate the content with other publication priorities. The planning of these papers will be handled by the SenNet Steering Committee Chairs (and/or full committee as needed) and due weight will be given to concerns and priorities of individual groups. SenNet PIs will take responsibility for planning for flagship papers well in advance of anticipated data release, ideally initiating the coordination of data release and publication 6 months in advance.
- Collaborative Project Papers
These manuscripts will be coordinated by SenNet members engaged in NIH-mandated collaborative projects. Authors are required to ensure that their papers do not conflict with plans for other papers and to bring any anticipated concerns to the SenNet Steering Committee.
- Other Papers
Authors are requested to ensure that their papers do not conflict with plans for flagship papers and collaborative project papers and to bring any anticipated concerns to the SenNet Steering Committee Chairs.
It will be the responsibility of the SenNet PIs to organize the content of the flagship papers and negotiate the content with other publication priorities. It is expected that individual research groups in SenNet will wish to publish results of their efforts in additional publications. These individual papers are anticipated to be primarily methodological in nature but may also describe biological insights that arise from TMC or UG3/UH3 analyses. Authors of collaborative project and other papers must actively identify and manage any conflicts with plans for Flagship papers. The SenNet Steering Committee Chairs (and/or full committee when needed) will determine the suitability of certain data and analyses for incorporation into a flagship vs an individual TMC or UG3/UH3 publication. Submissions for publication should be coordinated where possible in order to enhance impact. In all cases, consideration, co-authorship or, at a minimum, acknowledgement should be given to all SenNet members who contributed effort and/or materials to any publication. If released but unpublished data are to be used, then the SenNet Steering Committee Chairs may determine that submission of the TMC or UG3/UH3 manuscript must wait for the publication of the Flagship manuscript. SenNet research groups doing analyses that are similar to each other are encouraged to establish collaborations to coordinate the publication of research results.
In addition to abiding by data-confidentiality requirements, use of individual-level biomedical data requires compliance with the conditions of data use in the consent or authorization form for each tissue source (see SenNet Human Subject Policy) and data access, controlled-access data policies, and any journal requirements for data sharing compatible with internal data sharing policies and permissions.
Guidelines on Publications with Authors Outside of the Consortium
It is expected that SenNet members will produce joint publications with non-SenNet groups using only officially released data. These plans should be listed in the SenNet publication tracker. For external collaborations using SenNet data (specifically) the SenNet PI is expected to make sure that the external collaborators involved in joint publications agree to adhere to the SenNet External Data Use Agreement, confidentiality, and other policies. Notably, the SenNet External Data Use Agreement includes policy on publishing or publicly disclosing SenNet data prior to its official release by the Consortium. This includes notifying and receiving approval from the SenNet Steering Committee Chairs in advance. Groups can approach the SenNet Steering Committee Chairs with requests for exceptions as described below.
Exceptions and Concerns
Any concerns or requests for exceptions to these guidelines should be brought to the attention of the SenNet Steering Committee Chairs. Such exceptions or grievances may cover any topic area included in, or overlooked by, this policy e.g., challenges in submitting preprints, or in following SenNet policies in non-SenNet collaboration activities or other considerations like academic competition etc. The SenNet Steering Committee Chairs may refer the matter to the entire SenNet Steering Committee or seek external advice or mediation as needed.
All SenNet publications need to acknowledge funding through the NIH Common Fund and cite all appropriate grant numbers using the specific language: “This research is supported by the NIH Common Fund, through the Office of Strategic Coordination/Office of the NIH Director under awards X, Y, Z (grant number)”.
I, as the PI of a SenNet U54, UG3/UH3, or U24, will abide by and accept responsibility for distributing this policy to all members of my team and ensuring compliance of my team with this policy:
*This policy was adapted from the HubMAP Consortium Publication Policy https://hubmapconsortium.org/policies/publications-policy/ another NIH Common Fund Initiative.