October 7, 2019
This document provides publication guidelines for the HuBMAP Consortium (sometimes referred to in this document as simply “Consortium”) that have been agreed to by the entire Consortium through the Steering Committee. It covers the goals and guidelines that apply to authorship, acknowledgements, metrics tracking etc. related to the dissemination of HuBMAP supported products. It covers all products of the HuBMAP 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.
HuBMAP, like many other NIH programs, will follow “rapid data release” policies to the community. We will publish data release schedules (with a minimum frequency of every six months after the first release) on our website for the community’s benefit. Working papers and/or white papers generated by the HuBMAP 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 HuBMAP data will be released after “data verification”, which is defined as assessing the usability of the data. That is, the data has 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:
- Encourage collaborative work within the Consortium.
- Promote transparency and fairness within the Consortium (see authorship, stable identifiers, acknowledgment below) and with the wider research community.
- Guide and encourage communication within the Consortium 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 HuBMAP products FAIR, by using publicly available persistent identifiers for:
- authors (e.g., ORCID),
- data (e.g., DOI or HuBMAP 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 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 HuBMAP 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 Consortium Members
- Standard Operating Procedures - Internal and External Sharing
- All experimental SOPs used in HuBMAP will be made available on protocols.io
- “Publication” refers to products as defined above, including journal articles and major national or international scientific presentations.
- Journals with Open Access publication standards are preferred for all HuBMAP publications and required for Consortium-wide papers. Gold (made freely and immediately accessible by journal upon publication) or green (self-archiving) open access publication is acceptable. At minimum, authors need to comply with the NIH Public Access policy (https://publicaccess.nih.gov/).
- Internal Manuscript and Major National/International Presentation tracking
- Planned manuscripts & presentations must be logged on a Consortium tracker for preview by Consortium Members.
- The Consortium tracker records 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.
- It is expected, in order to encourage collaboration and coordination, that all publications will be reported here well in advance, preferably as the idea is generating.
- The Consortium tracker will provide a time stamp for abstracts and manuscripts and provide an internal timeline of development.
- The Consortium tracker will be used to identify conflicts and collaborative opportunities in publication plans that will be reviewed by the 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 Executive Committee.v
- Preprints must be complete manuscripts in form suitable for publication
- Citing of preprints, pending journal publication, is expected
The guiding principle for joint publications of the Consortium is to exploit the rich expertise of the consortium members to produce manuscripts that describe comprehensive, in-depth studies of human tissues at the cellular and molecular level driven by data sets generated by the Consortium. Beyond these joint publications, members of the Consortium 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.
The Consortium anticipates the following publication types:
- Flagship Papers
- Overall (consortium-wide)
- Organ-centric (consortium-wide or organ-specific collaborations)
These manuscripts will be coordinated across the whole consortium 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 manuscript publication will not cause a delay in data release. The planning of these papers will be handled by the Steering Committee and due weight will be given to concerns and priorities of individual groups. HuBMAP PIs will take responsibility for planning for flagship papers well in advance of anticipated data release beginning no later than April 2020.
- Collaborative Project Papers
These manuscripts will be coordinated by consortium 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 Executive 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 Executive Committee.
It will be the responsibility of the HuBMAP 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 the Consortium 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 Center analyses. Authors of collaborative project and other papers must actively identify and manage any conflicts with plans for Flagship papers. The Steering Committee will determine the suitability of certain data and analyses for incorporation into flagship vs individual center publication. Submissions for publication should be coordinated where possible to enhance impact. In all cases, consideration, co-authorship or, minimally, acknowledgement should be given to all Consortium members who contributed effort and/or materials to any publication. If released but unpublished data are to be used, then the SC may determine that submission of the Center manuscript will wait for the Flagship one. Consortium 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 tissue source consented conditions of data use 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 HuBMAP members will produce joint publications with non-HuBMAP groups using only officially released data. These plans should be listed in the Consortium publication tracker. For external collaborations using HuBMAP data (specifically) the HuBMAP PI is expected to make sure that the external collaborator is aware of HuBMAP data use agreement, confidentiality, and other policies and that they will be expected to follow these in the joint publication as well.
Groups can approach the HuBMAP Executive Committee 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 HuBMAP Executive Committee (via Dena.email@example.com, firstname.lastname@example.org or HuBMAP SC Co-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 HuBMAP policies in non-HuBMAP collaboration activities or other considerations like academic competition etc. The EC may refer to the SC or consult for external advice or mediation as needed
All HuBMAP 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”.