BD² Open Science Policy

External Data Users
Version 1: May 2026

Open science is core to the mission of BD² and a critical component of accelerating the progress toward our vision that all people with bipolar disorder thrive – all research supported by BD² must follow the BD² Open Science Policy. This document outlines the components of the BD² Open Science Policy that pertain to external users of BD² Data and BD² Biospecimens, including data collected through the BD² Integrated Network study (“Integrated Network Data”). Agreement to this policy is required to access these resources, and failure to adhere to these requirements may result in the termination of data and/or biospecimen access privileges for approved investigators and other investigators at their institution.

Note: BD²-funded investigators are required to adhere to the specific governance policies associated with their BD²-funded program, including compliance with the full BD² Open Science Policy. For further details, BD²-funded investigators should reach out to their respective program team at [email protected] or [email protected].

The list below briefly outlines the required components of the BD² Open Science Policy that must be adhered to by all users of BD² Data and Biospecimens. Detailed instructions on each item, as well as additional recommendations and guidelines, can be found in the sections that follow.

I. Preprint Requirement – All manuscripts must be deposited in an open-access preprint repository no later than the time of first submission to a journal.

II. Manuscript Sharing Requirement – All manuscripts must be published in a journal that is either fully open access or hybrid open access.

III. Acknowledgement Requirement – All preprints, manuscripts, and research outputs must correctly and accurately acknowledge BD² and BD² resources.

IV. Method and Code Sharing Requirement – All protocols and code used for analysis, experimentation, or data processing of BD² Data or Biospecimens must be made available in an open-access format.

V. Data and Resource Sharing Requirement – All data and resource outputs generated through the use or analysis of BD² Data or Biospecimens must be made available in an open-access format, except when not possible due to the requirement to protect sensitive human data.

To ensure compliance with these policies, external investigators who are using BD² Data are expected to communicate the following with BD²:

• After depositing to a preprint server, preprints must be sent to BD² ([email protected]) for an Open Science Compliance Check.
•  At least 30 days prior to final submission of a manuscript for publication, investigators must submit a manuscript draft and complete a BD² Publication Form, though which investigators will supply article links, persistent identifiers for resources, a lay summary of the work, and other details.

Detailed Open Science Policy Requirements for External Data Users

Definitions

• BD² Data: Any dataset that was collected through a BD²-funded effort
  • Integrated Network Data: BD² Data collected from the BD² Integrated Network Longitudinal Cohort Study. Because this dataset consists of human subject data, it requires completion of a Data Use Agreement and has additional layers of protection, noted in this policy in purple text.

• BD² Biospecimens: Any biological materials collected from participants in the BD² Integrated Network Longitudinal Cohort Study or other BD²-funded effort.
• BD² Manuscript: Any manuscript that is fully or partially funded by BD², including manuscripts that use BD² Data or BD² Biospecimens.

Index

I. Preprint Requirement – Page 2
II. Manuscript Sharing Requirement – Page 3
III. Acknowledgement Requirement – Page 4
IV. Method and Code Sharing Requirement – Page 4
V. Data and Resource Sharing Requirement – Page 5
     Appendix A: Additional Resources and Recommendations – Page 8

I. Preprint Requirement

All BD² Manuscripts that result from the use of BD² Data or BD² Biospecimens must have a version that is shared in an open-access preprint repository no later than the time the article is first submitted to a journal for consideration. Note that BD² will confirm this timing by comparing preprint deposition data to journal submission date, which is available in article metadata. Investigators must select the least restrictive license for the preprint, which in most cases will be a CC BY 4.0 or CC0 license type (see Appendix A for more details).

Acceptable preprint servers include bioRxiv and medRxiv, though any open-access repository that provides a persistent identifier, e.g., a digital object identifier (DOI), is acceptable. If a preprint is posted to bioRxiv, BD² may index it within our BioRxivChannel.

Once deposited, the persistent identifier and/or weblink associated with the preprint must be emailed to BD² at [email protected]. BD² will then perform an Open Science Compliance Check and provide a checklist of any updates that must be made prior to final formal publication of the manuscript.

Investigators are encouraged to make their preprint fully compliant with all components of the BD² Open Science Policy. BD² can facilitate this process, and investigators have the option to submit a draft version of their preprint for an Open Science Compliance Check prior to deposition onto a preprint server.

Minimum Requirements:

• All BD² Manuscripts must be preceded by an open-access preprint with a persistent identifier.
• All preprints must use a CC BY 4.0, CC0, or equivalent license type.
• All preprints must be sent to BD² for an Open Science Compliance Check and review.

Additional Recommendations:

• All preprints should be fully compliant with all components of the BD² Open Science Policy at the time of deposition to a preprint server.
• Investigators may request an Open Science Compliance Check from BD² on a preprint draft prior to deposition.

II. Manuscript Sharing Requirement

BD² Manuscripts must be published in a journal that allows for the option to make an article open access (see Open Policy Finder for journal-specific details). This includes fully open access journals, such as eNeuro or BMC Psychiatry, or hybrid open access journals that allow authors to pay an Article Processing Charge (APC) to upgrade their manuscript to open access. Open Access articles should select the least restrictive license – CC BY 4.0, CC0, or equivalent.

BD² Manuscripts should adhere to the full BD² Open Science Policy and, at a minimum, must comply with the requirements within this document. To ensure compliance, manuscripts must be emailed to BD² ([email protected]) at least 30 days prior to final submission to a journal. BD² recommends that after a manuscript has gone through an initial round of reviews and revisions, that a draft is sent to BD² for a compliance check – i.e., prior to “final” editorial review, at the point when authors expect an article to be accepted after only minimal further revisions.

For articles in hybrid journals that are fully compliant with the BD² Open Access Policy, BD² may support authors by covering Open Access APC fees in circumstances where the authors are unable to cover the fees. The authors may submit a request for BD² to cover Open Access APC fees to [email protected]. Requests will be considered only if compliance is met across the entire manuscript, not just the portion(s) that include BD² Data or BD² Biospecimens. BD², in its sole discretion, will determine if it is able to cover the costs of Open Access APC fees. Submission of a request does not guarantee payment. Investigators are encouraged to upgrade to open access, independent of BD² funding.

Once an article is accepted and in press, the authors must submit a BD² Publication Form. This form will request all article links, persistent identifiers for resources, a lay summary of the work, and other details at the discretion of BD². BD² will use this information as follows:

• Links to articles may be indexed within the BD² PubMed Central Collection.
• Persistent identifiers for the article and/or key resources may be indexed on a database on the BD² website, with the intent of making resources findable for the research community.
• The lay summary and other key findings may be used by BD² to publicize findings on our website, newsletter, and/or social media channels.

Minimum Requirements:

• All BD² Manuscripts must be published in an open access or hybrid access journal.
• All BD² Manuscripts must be sent to BD² ([email protected]) for an Open Science Compliance Checks at least 30 days prior to final publication; all components that result from the use of BD² Data must adhere to this policy.
• If BD² agrees to pay Open Access APC fees, the entire manuscript must be fully compliant with the full BD² Open Science Policy.
• Authors of accepted manuscripts must submit a BD² Publication Form.

Additional Recommendations:

• If published in a hybrid journal, authors should opt for open access APC fees.
• Articles should be made immediately available in an open-access format with no embargo period.
• Authors should select the least restrictive license (CC BY 4.0, CC0, or equivalent).
• Investigators may request additional and/or earlier Open Science Compliance Checks from BD² on draft versions of a manuscript.

III. Acknowledgement Requirement

All outputs associated with BD² Data or BD² Biospecimens must acknowledge the organization and any work by network personnel that went into collecting the data or biospecimens that were used. Outputs include BD² Manuscripts and preprints, as well as other resources such as code, protocols, datasets, and lab tools. The acknowledgement must be included in the formal Acknowledgements Section, or in the notes or detail area of a record if there is no specified place.

For BD² Manuscripts that use the BD² Integrated Network Data, authors must use the following language:
Data used in the preparation of this article were obtained from the BD² Integrated Network study [Dataset Version: INSERT VERSION #], sponsored by Breakthrough Discoveries for thriving with Bipolar Disorder (BD²; https://ror.org/00z5dw933). The authors acknowledge the efforts of the BD² Integrated Network Consortium members. The full list of current BD² Integrated Network Consortium members is available here: [https://www.bipolardiscoveries.org/consortium-members/]. For up-to-date information on the BD² Integrated Network study, visit bipolardiscoveries.org.

This language can be adapted as needed for other datasets or resources, ensuring the inclusion of “Breakthrough Discoveries for thriving with Bipolar Disorder (https://ror.org/00z5dw933)” and key resource identifiers with version information.

Minimum Requirements:

• All BD² Manuscripts and preprints must include BD² in the acknowledgements.
• All resources generated that are associated with BD² Data or BD² Biospecimens must include BD² in the acknowledgements.
• Any use of Integrated Network Data must use the exact language referenced above in acknowledgements.

IV. Method and Code Sharing Requirement

The details of any processes used to generate or analyze data from BD² Data or BD² Biospecimens must be made publicly available. This includes protocols, standard operating procedures (SOPs), and code, which must be shared using the guidelines outlined below:
Protocols: Any experimental method used to collect or analyze BD² Data or BD² Biospecimens, must be described in detail and made publicly available using a protocol sharing service, such as protocols.io or bio-protocol. The following guidelines must be adhered to:

• Protocols must be open access, have a persistent identifier, and use the least restrictive license.
• BD² Manuscripts must include a citation for each protocol and the use of a Key Resource Table is recommended. Investigators using Integrated Network Data must cite the Longitudinal Cohort Study Protocol [https://pubmed.ncbi.nlm.nih.gov/41428166/].

• Protocols related to Integrated Network Data must be reviewed a centrally by the BD² team ([email protected]) prior to posting and must not include details that may compromise the privacy of study participants or impede study objectives.

Code: Any code used in the analysis of BD² Data (including data processing, visualization, and computation) and any code developed or trained using BD² Data must be made publicly available according to the following guidelines:

• Code must be open access, with two versions recommended to be shared:
  • “Living” version – active version that may be further updated (e.g., GitHub URL; note this is not a persistent identifier).
  • “Archive” version – point-in-time archive of the code that was used for the manuscript (e.g., copy of code posted to Zenodo; see instructions); note this is a persistent identifier.
• BD² Manuscripts must include a citation for each set of code, and the use of a Key Resource Table is recommended.

  • Code that is used to analyze Integrated Network Data must be reviewed centrally by the BD² team ([email protected]) prior to posting and must not include details that may compromise the privacy of study participants or impede study objectives.

• If researchers are unable to share code due to restrictions on IP or commercialization concerns, they may request a waiver from BD². This request must be submitted prior to starting any code-based workflows and may preclude access to BD² Data or BD² Biospecimens. Reach out to [email protected] to initiate the waiver request process.

Minimum Requirements:

• All protocols and code used in relation to BD² Data or BD² Biospecimens must be publicly available.
• Persistent identifiers for all relevant protocols and code must be obtained and cited in any published manuscripts for which they were used.
• For protocols and code related to Integrated Network Data, the BD² team must review all links prior to their public release.

Additional Recommendations:

• All protocols and code in BD² Manuscripts and preprints should be publicly available (not just those associated with BD² Data or BD² Biospecimens).
• A list of protocols and code should be included in a Key Resource Table for all BD² publications.
• Protocol and code sharing should follow best practices to promote re-use (see Appendix A).

V. Data and Resource Sharing Requirement

Any research outputs newly generated under the support of BD² funding, including via the use of BD² Data or BD² Biospecimens, must be shared in a publicly accessible repository. Research outputs include datasets, cell lines, antibodies, software, and other materials developed for experimental use. For users of BD² Integrated Network Data,note that the ownership of any derivative product resulting from the manipulation, harmonization, aggregation, or analysis of that dataset will rest with BD².

Research outputs must be shared in an open-access repository no later than the time of output publication according to the guidelines below.

Datasets: Any original data generated using BD² Data or BD² Biospecimens must be made publicly available, except for human-derived data that may contain Protected Health Information (PHI). Data sharing must adhere to the following guidelines:

• Data must be open access, have a persistent identifier, and use the least restrictive license.
• BD² Manuscripts must include a citation for each dataset, and the use of a Key Resource Table is recommended.
• Data sharing should use an appropriate repository for the associated modality:
  • Basic tabular data can be shared on Zenodo. Investigators using BD² Data can request to post within the BD² community index on Zenodo.
  • More complex datatypes should use the field recommended format and repository (e.g., DANDI Archive for neurophysiology data and Brain Image Library for microscopy images).
  • Human-derived datasets, including from iPSCs and post-mortem tissue, must be de-identified (such that they retain no direct or indirect identifiers and no PHI) and shared with a public data repository in a manner that is as open as possible but as closed as necessary.
• Data sharing requirements pertain both to raw data and any processed or clean data, i.e. the data points represented graphically within a manuscript.

• Data resulting from analysis of Integrated Network Data must be reviewed centrally by the BD² team ([email protected]) prior to posting and must not include details that may compromise the privacy of study participants or impede study objectives.

Research Tools: All laboratory resources developed using BD² Data or BD² Biospecimens must be made available to the research community. This includes antibodies, cell lines, technological tools, software, and other research equipment, which must be shared according to the following guidelines:

• Researchers must catalog new resources with appropriate registries to obtain RRIDs and DOIs where applicable and cite these identifiers in BD² Manuscripts.

Minimum Requirements:

• All research outputs generated using BD² Data or BD² Biospecimens must be made publicly available.
• Persistent identifiers for all research outputs must be obtained and cited in any published manuscripts for which they were used.
• For research outputs related to Integrated Network Data, the BD² team must review all links prior to their public release.

Additional Recommendations

• All datasets and other research outputs in BD² Manuscripts and preprints should be publicly available (not just those associated with BD² Data or BD² Biospecimens).
• A list of research outputs should be included in a Key Resource Table for all BD² publications.
• Data sharing should follow best practices to promote re-use (see Appendix A).

Appendix A: Additional Resources and Recommendations

Endorsements:
The development of the BD² Open Science Policy leveraged guidelines set forth by several organizations whose efforts aim to improve open access among the research community. BD² endorses the following organizations and efforts:

• cOAlition S – This coalition of organizations endorses Plan S, an initiative that promotes open access publication of research funded by public grants.
• FAIR Principles – These guidelines promote research data to be findable, accessible, interoperable, and reusable.
• Panton Principles – These principles promote open access to research data to allow for the analysis, processing, and sharing without financial, legal, and technical barriers.
• SfDORA – The Declaration on Research Assessment promotes eliminating journal-based metrics, assessing merit-based research rather than journal reputation, and improving publication requirements to improve research.

Licenses:
All preprints, manuscripts, protocols, and datasets that are funded fully or partially by BD² are expected to be assigned a license that allows for reuse. The definitions below outline the different types of licenses that can apply.

• CC BY 4.0 is the default license required for all research papers. This license ensures that authors receive attribution for the work but allows work to be freely shared (i.e., redistributed in any medium or format or adapted for future purposes).
• CC0 is applied to authors employed by the government or to other content in the public domain. Under this license, no attribution is required.
• BD² does not allow CC-BY-ND or CC BY-NC-ND as licensing options for BD² Manuscripts with primary data published by investigators within the network. These licenses are not open-access licenses, as they do not permit adapting, transforming, translating, or updating the work.
• For more information licenses, including why non-commercial licensing is not allowed, please read the rationale from cOAlition S under the header “Licenses”.

Best Practices in Resource Sharing
Because resource sharing is done with the expectation of re-use, BD² encourages all researchers to consider FAIR principles when creating and annotating resources. FAIR resources are Findable, Accessible, Interoperable, and Reusable (see more details here).

Additionally, resource-specific best practices are as follows:

• Protocols:
  • Use “recipe style” formatting, detailing step-by-step instructions, and include “working” or “hidden” knowledge to promote effective use.
  • Use clear identification of experimental resources through the citation of persistent identifiers, such as DOIs, Resource Research Identifiers
    (RRIDs), and Chemical Abstracts Service (CAS) numbers; supplier catalog numbers and URLs are not considered persistent identifiers. BD² recommends using the Resource Identification Portal for locating identifiers.
  • Protocols can be versioned or forked to provide updates in a manner that keeps each version linked.
• Code:
  • Include documentation such as installation instructions and a README file with metadata and version notes.
  • Annotate code with usage notes, instructions, and other key details.
• Datasets:
  • Include a README file with all metadata necessary to understand, assess, and replicate the reported study findings.
  • Standardize data formats according to field-specific recommendations. Basic tabular data should use tidy data format, and all formats should be machine-readable.
  • Use clear and descriptive labels, both for the dataset and for the file names.