Data Archiving and Permissions

01 Data availability statement

Every empirical research manuscript must include a data-availability statement. It explains where the data supporting the results can be found, or the conditions under which they can be accessed when restrictions apply. Typical statements read:

• Data in a repository: “The data that support the findings of this study are openly available in [repository] at [DOI or accession number].”
• Data on request: “The data that support the findings of this study are available from the corresponding author on reasonable request.”
• Restricted data: “The data are not publicly available because of [legal, ethical or agreement-based restrictions] and are available from the corresponding author under [stated conditions].”
• Data in the article: “All data generated or analyzed during this study are included in this article and its supplementary files.”

02 Sequence and omics data

Nucleotide sequences are deposited in an INSDC database (GenBank, ENA or DDBJ), expression data in GEO or ArrayExpress, proteomics data in PRIDE or ProteomeXchange and metabolomics data in MetaboLights. Accession numbers are given in the article, and records are released no later than publication of the article. Data follow the FAIR principles and the minimum-information standard for the data type, for example MIAPPE for plant phenotyping.

03 Other data and repositories

Other data, such as raw images, measurements and phenotyping datasets, are deposited in a general-purpose or discipline-specific repository that assigns a persistent identifier, for example Zenodo, Figshare, Dryad or the Open Science Framework, so that they can be cited.

04 Code and software

Custom code, statistical analysis scripts and software used to produce the results are shared where possible, for example through Zenodo, GitHub or GitLab, with version numbers, dependencies and enough documentation to reproduce the analysis.

05 Plant resources

Seed stocks are deposited where practicable in a recognized germplasm collection, with accession numbers given for reproducibility. Voucher specimens for taxonomic and field studies are deposited in a recognized herbarium with collection information. Molecular constructs are deposited in a public repository such as Addgene, with plasmid maps and sequence verification.

Research on genetic resources reports compliance with access and benefit-sharing rules, including the Nagoya Protocol where it applies, with permit numbers and material transfer agreements where required, and CITES compliance for protected species.

06 People and privacy

Data from human participants, including ethnobotanical surveys, are shared only when this is consistent with the participants’ consent and the ethics approval for the study. Authors remove information that could identify a person, and follow applicable data-protection law. Knowledge shared by communities is reported with their consent.

07 Permission to reuse published material

A manuscript that reproduces figures, tables or substantial text published elsewhere needs written permission from the copyright holder, usually the original publisher. Authors supply the permission with the submission and give the source in the caption, for example “Adapted with permission from [citation]”. Material published under CC BY needs attribution but usually no permission.

JAPB articles are published under CC BY 4.0, so they can be reused without asking permission, provided they are credited as set out on the Copyright and License page.

08 Supplementary material

Supplementary files, such as extended tables, uncropped gel images, questionnaires, datasets or video, are welcome. Each file is clearly named, for example “Supplementary_Table_1.xlsx”, and briefly described in the manuscript. Supplementary material is reviewed with the manuscript and published as supplied.

09 Questions

For questions about data sharing or permissions, write to the editorial office at info@openaccesspub.org.