Repository and Identifiers

Use this file when selecting repositories, checking accession strategy, or writing dataset citations.

Repository decision tree

Use a mandated repository when the data type requires it.
If no mandate applies, use a discipline-specific, community-recognised repository.
If no domain repository fits, use a trusted generalist or institutional repository that provides persistent identifiers and durable metadata.
Do not use personal websites, lab websites, ad hoc cloud folders, or unpublished private drives as the only availability route.
For very large data, use a repository or institutional infrastructure that can preserve metadata and provide clear access instructions even if bulk files require special transfer.

What a repository record should provide

persistent identifier: DOI, accession, Handle, ARK, or equivalent stable record
public landing page with title, creators, abstract/description, repository, date, version, licence
file list with sizes and formats
README or data dictionary
provenance and processing description
relation to the manuscript and related code
clear access procedure for restricted data
versioning or update policy

Common repository categories

Choose according to field norms; this list is not exhaustive.

Data type	Typical repository pattern
Sequencing / gene expression	GEO, SRA, ENA, ArrayExpress or field-specific omics archive
Protein/nucleic acid structures	wwPDB / PDB
Small-molecule crystallography	CCDC or other crystallographic archive required by the journal
Proteomics	PRIDE or ProteomeXchange member repository
Metabolomics	MetaboLights or domain archive
Neuroimaging	OpenNeuro, DANDI, NDA, or controlled-access archive when required
Clinical or sensitive human data	controlled-access repository such as dbGaP, EGA, controlled institutional archive, or data access committee
Earth/environment/space science	PANGAEA, NASA/NOAA/ESA data centres, domain observatories
Social science	ICPSR, Dataverse, UK Data Service, OpenICPSR, OSF where appropriate
General datasets	Dryad, Zenodo, Figshare, OSF, institutional repository with DOI support

Always check the target journal and funder because some data types have mandatory repositories.

Identifier rules

Prefer final public identifiers before submission.
If the record is private during review, provide an anonymous reviewer link when the repository supports it.
Do not cite temporary sharing links as dataset identifiers.
Include accession numbers exactly as assigned by the repository.
Use one identifier per coherent dataset record; avoid burying unrelated data under one unclear DOI.
Version datasets when files change after review or publication.
If the dataset has a DOI, cite the DOI rather than only the repository URL.

Dataset citation pattern

Dataset references should include the minimum DataCite-style elements:

[Creator(s)] ([Publication year]) [Dataset title]. [Repository]. [Identifier].

Add version when meaningful:

[Creator(s)] ([Year]) [Dataset title], version [version]. [Repository]. [DOI/accession].

For reused public data, cite the dataset in the reference list when the dataset supports conclusions. Mentioning it only in the Data Availability statement may be insufficient.

Repository readiness checklist

Before submission:

DOI/accession resolves to the intended landing page
title matches manuscript terminology
creators and affiliations are correct
licence is present and compatible with intended reuse
files open without proprietary software where possible
README explains columns, units, missing values, transformations, and scripts
figure source data are clearly mapped to figure panels
restrictions and access conditions match the manuscript statement
embargo/private links have been tested outside the author account

Red flags

"Data available on GitHub" without release DOI or archive
repository record has no licence
uploaded zip file has no README or file manifest
accession exists but is not public, not under embargo, and not available to reviewers
filenames use local analysis shorthand that readers cannot interpret
manuscript cites one dataset but results depend on several unlisted secondary sources

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