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文档润色流和知识库构建流/claude-scholar/skills/nature-data/references/repository-and-identifiers.md

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+# Repository and Identifiers
+
+Use this file when selecting repositories, checking accession strategy, or writing dataset
+citations.
+
+## Repository decision tree
+
+1. Use a mandated repository when the data type requires it.
+2. If no mandate applies, use a discipline-specific, community-recognised repository.
+3. If no domain repository fits, use a trusted generalist or institutional repository that provides
+   persistent identifiers and durable metadata.
+4. Do not use personal websites, lab websites, ad hoc cloud folders, or unpublished private drives as
+   the only availability route.
+5. 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:
+
+```text
+[Creator(s)] ([Publication year]) [Dataset title]. [Repository]. [Identifier].
+```
+
+Add version when meaningful:
+
+```text
+[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