CBI Guidelines for Authorship and Acknowledgments

Guideline Development

Peer-reviewed scientific publications are a vital way for our CBI team to communicate our research findings to Department of Energy (DOE) sponsors, the scientific community, and the broader public. A clear definition of what is required for manuscript development and authorship will aid in ensuring that we fairly credit individual research and intellectual contributions, facilitate trust among team members and collaborators, and enable our institutions and funding agencies to identify and track scientific contributions for each study.

The Center for Bioenergy Innovation (CBI) has a diverse range of researchers, and thus, considerations for authorship, emphasizing our integrated team science across multiple institutions, scientific disciplines, and career stages is needed. We also have an expectation from our DOE sponsors for early and open sharing of data generated by the project. The following authorship guidelines were developed based on criteria from Science and Nature, as well as through the evaluations of guidelines in place for our home institutions and other large, multi-institutional, DOE-funded projects (here, we largely model the guidelines outlined by the NGEE Arctic project (DOI: 10.15485/2588111).

The primary goals of the CBI authorship guidelines are to provide:

Transparency for what constitutes authorship
Fairness among research contributors and collaborators
Accessible ways to ‘opt-in’ to manuscript development
Mentorship and support of early career team members

These guidelines serve as a framework for considerations at each stage of manuscript development, including planning, execution, writing, and publication. These guidelines foster clear expectations for transparency and appropriate inclusion of current and legacy contributors to a given manuscript, including early and continuing discussions on authorship and acknowledgements within the broader pool of potential contributors (including students and technicians) that merit co-authorship. Guidance on authorship disputes and acknowledgements are also included.

Please note that exclusion from authorship of individuals who have made author-level contributions is not permitted within CBI, nor is gratuitous authorship (e.g. PI of contributing author that made no contributions to experimental design or manuscript development).

Manuscript Planning

It is requested that you do the following when planning a manuscript:

Read the Authorship Guidelines. These guidelines, as well as those for other professional societies and your home institutions, will ensure the most impactful and equitable publications for all members of CBI.

Maintain Continual Communication. Include your planned manuscript (and expected submission date) in the CBI publication spreadsheet as “In Prep” prior to beginning manuscript development (i.e., when you’re starting to develop a research plan for a target project). Planned papers are not fixed and SHOULD be adjusted as needed, but this exercise is important for transparency across the CBI team and accountability for promised task deliverables.

Read the CBI Data Policy. Project data are expected to be shared as soon as possible following the CBI Data Management Plan. While data sharing is key to open science practices, it is vital for the CBI team to appreciate, acknowledge, and reward the efforts of data collection teams by offering co-authorship where appropriate.

Manuscript Development

It is requested that you develop or participate in a manuscript according to the following guidelines:

As the Lead Author(s):

Be Proactive. The lead author should be proactive with contributors and other collaborators, offering co-authorship when contributors are considered appropriate and able to make meaningful contributions. If CBI project data or data from CBI sites are fundamental to the development of a manuscript, the data owners should be offered the opportunity to contribute substantively as co-authors, even if the data are publicly available. This follows practices such as the AmeriFlux Data Use Policy.

Define What Constitutes Authorship. The lead author is responsible for defining authorship in a fair and equitable manner, and is highly encouraged to clearly communicate the responsibilities of co-authors when involving them in a project and actively updating the manuscript and authorship status in the CBI publication spreadsheet. It is recommended to continually evaluate contributor roles as specified by the Contributor Role Taxonomy (CRediT), with annotated additions from the CBI team (see Table 1). The lead author is responsible for careful review of these roles to warrant authorship and consistent attribution among co-authors. It is also recommended that each co-author play at least two contributor roles and additionally review the manuscript prior to submission. Minor contributions (e.g., allowing access to a piece of shared equipment without considerable input on experimental design or troubleshooting, or sharing previously published data or software algorithms without intellectual input or only providing casual feedback) do not warrant authorship. If co-authorship is unclear or controversial, please contact CBI team leadership. If a team member or collaborator does not meet criteria for authorship, it is requested that you credit their contributions in figure legends, photo credits, data or software citations, or acknowledgements. Author contributions should be specified in the manuscript as directed by the chosen journal, but if more than one funding source is utilized, specific contributions of authors on those funding sources should be outlined accordingly in the Acknowledgements or Author Contribution sections (depending on journal guidelines).

Consider the Data Life Cycle. Although DOE sponsors mandate timely publication of generated datasets, there is often a period between data collection and when data are made publicly available to ensure careful curation. Therefore, use of an unpublished dataset requires written approval from data owners and consideration for co-authorship. Additionally, publicly available data not yet used in a publication by the data owners may exist for CBI research. In this case, CBI team members should include data owners in at least the primary paper that uses their data, but not all following papers unless contributions align with CBI guidelines.

Communicate Regularly and Be Transparent. The lead author should communicate regularly about progress and updating the CBI publication spreadsheet, including sharing drafts of analyses, figures, and text as often as is productive or requested by co-authors, keeping versions and associated material in a shared folder. The expectation of the lead author is to ensure they maintain clear and regular communication with data owners to make sure the data are used and interpreted appropriately and contributors have clear expectations for what is expected from each individual in completing a draft. When a draft manuscript is completed, the lead author must circulate the draft among all co-authors and consider comments and changes. The draft manuscript must be reviewed and approved by each co-author before submission; note that individual institutions may require additional reviews before submission. The lead author must also make co-authors aware of any feedback from the journal editor or reviewers and allow time and opportunity for co-authors to read and contribute to manuscript revisions or responses to reviewers. Each co-author is expected to review and approve the revised manuscripts before resubmission.

Consider Data Accessibility. Prior to or adjacent with manuscript submission, datasets are expected to be made available in a public, long-term data repository associated with the appropriate DOE funding source. CBI has developed a dataset workflow to assist in developing and submitting datasets for data DOIs. Original and derived datasets should be cited in the ‘References’ section of a manuscript whenever possible, though this may depend on journal policy. Acknowledgement and Data Availability sections may include general information about where and how to access the data, but this does not exclude inclusion in the ‘References’ section when possible.

As Co-Authors or Potential Co-Authors:

Opt-In. Potential co-authors should signal their interest in opting into a developing manuscript in the CBI publication spreadsheet and by emailing the lead author. Note that this begins a discussion on what would merit co-authorship on a paper – authorship is not guaranteed. Aligned with our definition of authorship above, potential co-authors should identify their responsibilities with the lead author to ensure active and meaningful engagement in and accountability for the research (Table 1).

Be Responsible. Co-authors should follow responsibilities defined with the lead author, be personally accountable for their own contributions, and ensure that the research and the data are correct and appropriately presented and interpreted. Co-authors are also expected to provide timely feedback and/or assistance when requested by the lead author. Co-authors are also encouraged to communicate with the lead author regularly, participating in both scientific and logistical discussions. Co-authors should recognize that final decisions on data inclusion and interpretation, as well as writing, belong to the lead author. This responsibility and freedom are particularly important to communicate when the lead author is an early-career scientist. Co-authors should not delay the research or manuscript submission progress.

As CBI Team Members:

Use Artificial Intelligence Ethically and Transparently. Generative artificial intelligence (GenAI) is becoming broadly available. However, authors should adhere closely to guidance provided by their home institution and the broader scientific community for the use of GenAI in their research and subsequent manuscripts. A growing number of peer-reviewed journals now explicitly state that GenAI is not permitted as a co-author as it cannot take responsibility for the integrity of the manuscript, and if GenAI tools are used in the development of graphical elements, text, or data, they must be clearly acknowledged in the manuscript. Therefore, we suggest that GenAI tools are used on a limited basis (e.g., brainstorming, language refinement, checks for grammatical or typographical errors, summarizing text, code assistance) and with critical oversight. Any output using GenAI tools requires additional proofreading by the authors. This guidance may not apply to other aspects of AI technology (e.g., machine-learning) which are often used as statistical or modeling tools and which should be clearly described in the Materials and Methods section.

Be accountable. All manuscript co-authors are responsible for the content of the manuscript, especially any portions that may have been developed in collaboration with an AI tool.

Share These Guidelines With Others. When a CBI team member is involved in an external manuscript using data from CBI research, the team member is encouraged to share our authorship guidelines with the lead author to set expectations and facilitate discussion.

Manuscript Publication

Once a manuscript has been accepted by a journal, we request that you:

Let Us Know. Congratulations! Notify your Team Lead and CBI Management so we can include your accomplishment in newsletters and reports. The easiest way to record this is in the Dropbox paper for your team.

Confirm Data Availability. Confirm that all data associated with the publication are currently publicly available or will be publicly available by the time of manuscript publication in agreement with CBI Data Guidelines, and that correct references and valid links are provided.

Add to Our Publication List. Add your manuscript to the Dropbox Paper document with published doi and John Wagner will add to the master CBI publication list.

Authorship and Citation Consideration Criteria:

All authors are expected to have made substantial contributions to two or more of the following: conceptualization, data curation, formal analysis, funding acquisition, investigation, methodology, project administration, resources, software, supervision, validation, visualization, and writing, reviewing & editing [Ref: htts://credit.nico.org/].
All authors are expected to have approved the submitted version, as well as any substantially modified version that involves the author’s contribution to the study.
The lead and senior/corresponding authors are responsible for ensuring the 1) accuracy or integrity of the work, including co-authorship and 2) that any questions related to accuracy or integrity are investigated and resolved.
Co-authorship is appropriate for the development of unique and nontrivial resources on which the work depends, e.g., GWAS populations, SNP libraries, common gardens, databases, genetic reagents, etc. However, co-authorship is extended only for the first-time a given resource or dataset is used in a CBI publication; subsequent co-authorship should not necessarily be extended to future papers unless there is a direct or new contribution to the manuscript.
Data products such as SNP libraries, expression data, geolocated populations, etc. should be published as data DOI’s simultaneously with the manuscript submission. These DOI’s should be referenced in subsequent publications. Similarly, software products used in analysis, including version numbers should be referenced via their respective DOI’s.
Lead and senior/corresponding authors should actively work to avoid citation bias [Ref: https://pubmed.ncbi.nlm.nih.gov/32762966/]. CBI publications should cite the most relevant publication internal or external to CBI.

Individuals who have participated in generation of the work/reagents/resources but who do not meet the criteria for authorship should be listed in the acknowledgments section with a brief indication of the nature of their contribution.

Required Acknowledgments

Please include project-relevant keywords in your submitted manuscript so that CBI science is easily indexed and searchable. Please also acknowledge the project, adding additional projects, institutions, or people as appropriate. The following is the acknowledgements template to use for CBI-sponsored publications:

“This material is based upon work at the Center for Bioenergy Innovation supported by the U.S. Department of Energy, Office of Science, Biological and Environmental Research under Contract Number ERKP886.”

If you have used JGI for DNA/RNA sequencing or DNA synthesis please include this acknowledgment:

“The sequencing work was conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.”

Authorship Disputes

Authorship disputes involving CBI team members (not solved at the level of the lead author) should be directed to CBI Chief Science Officers, Carrie Eckert and Melissa Cregger. Disputes will be mediated in facilitated conversations that may include co-authors, institutional leaders, external collaborators, and journal editors and will be informed by journal policy. From this, the dispute will be brought to a resolution, with recommendation going to the CEO, Gerald Tuskan, for final decision.

CBI Predatory Journal Considerations

Concerns exist for the increasing proliferation of “predatory journals.” These may be defined as “pay to publish with minimal editorial scrutiny.” Similarly, there are “predatory conferences” which seek to use your reputation to bolster their attendance and profits. Some of these even list researchers as editors, organizers or “invited” speakers without their awareness or permission.

As you consider where to submit your research, consider the journal’s listing in major databases (e.g., PubMed, WebSci, Scopus) and impact factor, although these can be inflated by the practices of predatory journals. For new journals, consider the publisher, the recent publications, and how you heard of the journal or conference (i.e. an unsolicited email). A good rule of thumb is to submit your research to Society-sponsored journals supported by professional societies, non-profits, or academic institutions (e.g., American Chemical Society, Royal Society) that are peer-reviewed and focus on high-quality research to promote science rather than just for profit, and often provide member benefits including discounted publishing or free access.

If unsure, consult with your coauthors and colleagues. We trust your judgment on this issue. If you wish to investigate more, here are some reputable links.

Table 1. Contributor roles adapted for CBI (based on the Contributor Role Taxonomy (CRediT))

Contributor Roles	Definition
*Conceptualization*	Formulation or evolution of overarching research goals and aims. May also include ‘intellectual contribution’ to a manuscript, including edits that reframe or improve upon existing ideas and analyses.
*Data Collection, Curation, and Interpretation*	Conducting research, specifically performing experiments or data collection, collation, and interpretation, as well as data annotation for initial use and later re-use.
*Formal Analysis*	Application of statistical, mathematical, computational, or other formal techniques to analyze or synthesize study data.
*Funding Acquisition*	Acquisition of the financial support for the project leading to the manuscript.
*Methodology*	Development or design of methodology, experimental design; creation of models.
*Project Administration*	Management and coordination responsibility for the research activity planning and execution.
*Resources*	Provision of study materials, reagents, materials, laboratory samples, instrumentation, computing resources, or other analysis tools.
*Software*	Programming, software development; designing computer programs; implementation of the designed computer code and supporting algorithms; testing of existing code components.
*Supervision*	Oversight and leadership responsibility for the research activity planning and execution, including mentorship external to the core team.
*Validation*	Verification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs.
*Visualization*	Preparation, creation and/or presentation of the published work, specifically visualization/data presentation.
*Writing – Original draft*	Preparation, creation and/or presentation of the published work, specifically writing the initial draft (including substantive translation).
*Writing – Review & Editing*	Preparation, creation and/or presentation of the published work by those from the original research group, specifically critical review, commentary or revision – including pre- or post-publication stages.