@researai/deepscientist 1.5.16 → 1.6.0

package/src/skills/nature-data/references/fair-metadata-checklist.md

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+# FAIR Metadata Checklist
+
+Use this file to audit whether a dataset deposit is findable, accessible, interoperable, and
+reusable enough for a Nature-style submission.
+
+## Quick FAIR test
+
+| Principle | Practical check |
+|---|---|
+| Findable | Dataset has a persistent identifier, rich title/abstract/keywords, searchable repository record, and metadata that names the data identifier. |
+| Accessible | Identifier resolves through a standard protocol; access conditions are explicit; metadata stay public even if data are restricted. |
+| Interoperable | Files use community formats where possible; metadata use shared vocabulary, units, identifiers, and qualified links to related data/code/publication. |
+| Reusable | Licence, provenance, methods, variables, quality-control notes, version, and community-standard metadata are clear enough for reuse. |
+
+## DataCite core fields
+
+Mandatory fields commonly expected for DOI-style dataset records:
+
+- Identifier
+- Creator
+- Title
+- Publisher / repository
+- Publication year
+- Resource type
+
+Strongly recommended when available:
+
+- contributor and role
+- description / abstract
+- subject keywords
+- funding reference
+- related identifiers: manuscript preprint/article, code repository, protocol, previous dataset
+- version
+- licence / rights
+- geolocation or temporal coverage for spatial/temporal data
+- language
+
+## Dataset README template
+
+```text
+# [Dataset title]
+
+## Summary
+[One-paragraph description of what the dataset contains and which manuscript results it supports.]
+
+## Files
+- [filename]: [contents, format, size, related figure/table]
+
+## Variables and units
+[Column/field name] | [definition] | [unit] | [allowed values/missing-value code]
+
+## Methods and provenance
+[How data were generated, collected, transformed, filtered, normalised, or aggregated.]
+
+## Software and environment
+[Software, package versions, scripts, notebooks, operating system or instrument software when relevant.]
+
+## Access and licence
+[Licence, access restrictions, data-use agreement, embargo, or controlled-access process.]
+
+## Citation
+[Preferred dataset citation.]
+```
+
+## File organization
+
+- Use stable, descriptive filenames instead of local shorthand.
+- Keep raw and processed data separate.
+- Include a manifest for archives or large multi-file deposits.
+- Map source data to exact figure panels and table numbers.
+- Preserve units in column names or data dictionaries, not only in manuscript captions.
+- Record missing-value codes and filtering decisions.
+- Include checksums for large or critical files when the repository does not generate them.
+
+## Provenance prompts
+
+Ask the author:
+
+- What instrument, survey, simulation, database, or processing pipeline produced each file?
+- Which script or notebook converts raw data into each figure or statistical table?
+- Which samples, time points, conditions, or participants were excluded, and why?
+- What version of each third-party dataset was used?
+- Are there licences, consent forms, data-use agreements, or ethics approvals that limit reuse?
+- Has any data been transformed in a way that prevents reconstruction of the raw values?
+
+## Licence guidance
+
+- Prefer a standard open licence when data can be public.
+- Use the repository's licence field rather than only writing licence text in the manuscript.
+- Use CC0 or CC-BY-style terms only when appropriate for the data and institution.
+- Do not apply an open licence to third-party or participant data unless the authors hold the right
+  to do so.
+- For code, use a software licence and archive a release when possible.
+
+## Final audit
+
+Block submission until these are resolved:
+
+- no Data Availability statement for original research
+- no identifier or stable access route for data supporting central conclusions
+- sensitive data restriction without access procedure
+- third-party data with no source or permission route
+- public dataset with no licence or README
+- claim that data are in the paper when figure source data are absent
+- mismatch between manuscript statement, repository record, and supplementary files

package/src/skills/nature-data/references/policy-principles.md

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+# Policy Principles
+
+Use this file when deciding what a Nature-ready data statement must disclose.
+
+## Governing rules
+
+- Every original research article needs a Data Availability statement.
+- The statement must say what supporting data exist, where they can be found, and any access
+  conditions.
+- The statement must cover data generated by the study and secondary data reused for analysis.
+- Public repository deposition is preferred. For community-mandated data types, use the required
+  repository.
+- Reviewers may need access to underlying data and code during evaluation.
+- Restrictions are allowed only when they are justified and disclosed. Privacy, consent, endangered
+  locations, third-party licences, commercial restrictions, and national law are common reasons.
+- Restricted data still need a durable access route: named data access committee, institution,
+  controlled-access repository, application procedure, or responsible group.
+- The statement should not hide key evidence in vague language such as "data available upon
+  reasonable request" unless the reason and process are explicit.
+
+## Minimal dataset test
+
+Ask whether an independent reader can inspect or reproduce the paper's central findings from the
+available material.
+
+Include:
+
+- source data for main figures and key supplementary figures
+- raw or sufficiently reusable data, according to community norms
+- processed data used for statistics, plots, model training, or validation
+- analysis-ready tables if raw data require specialized transformation
+- third-party datasets with source, version, date accessed when relevant, and licence/access terms
+- representative metadata for restricted datasets, even when records themselves cannot be public
+
+Exclude only when defensible:
+
+- data that were not used to support a result
+- purely theoretical work that generated or analysed no dataset
+- identifiable human data that cannot be anonymised or shared under consent and law
+
+## Availability routes
+
+Use one route per dataset or dataset family.
+
+| Route | Use when | Statement must include |
+|---|---|---|
+| Public repository | Data can be openly shared | repository, DOI/accession, dataset title or scope, licence if known |
+| Controlled repository | Data are sensitive but discoverable | repository, accession/record, access committee or procedure, restrictions |
+| Supplementary/source data | Small supporting files are hosted with paper | exact file/table/source-data mapping |
+| Reused public data | The study analyses existing public data | original repository/source, identifier, version/date accessed if needed |
+| Third-party restricted | Data are licensed or owned by another party | owner/source, why not public, request route, permission condition |
+| Request-based access | No repository route is possible | reason, responsible group, eligibility, expected conditions, contact route |
+| Not applicable | No datasets were generated or analysed | concise reason; do not use for studies with any empirical data |
+
+## Data, code, materials, protocols
+
+Data Availability is not a substitute for code, materials, or protocol availability.
+
+- Put custom code in a Code Availability section when the journal separates it.
+- Mention code in Data Availability only when it is bundled with the dataset and needed to interpret
+  files.
+- For unique biological materials, reagents, cell lines, plasmids, or model organisms, use
+  persistent identifiers where available and state distribution restrictions separately.
+- For protocols, cite protocol repositories or include enough method detail for reproducibility.
+
+## Sensitive and human-participant data
+
+For sensitive data, preserve transparency without breaching consent or law.
+
+State:
+
+- why open sharing is not possible
+- whether anonymised, aggregate, synthetic, or representative data can be shared
+- where metadata or a summary record is available
+- who reviews access requests
+- what approval, data-use agreement, or ethics condition applies
+- whether access is limited to non-commercial, academic, local-jurisdiction, or qualified users
+
+Avoid:
+
+- naming a single individual as the only durable access route when an institutional route exists
+- implying data are available if access depends on impossible or undefined permissions
+- promising public release later without a repository, date, and responsible party
+
+## Submission-stage checks
+
+Before finalizing, confirm:
+
+- all accession numbers, DOIs, and URLs resolve
+- embargoed/private reviewer links work anonymously where required
+- restricted data metadata records are public if the records themselves are not
+- supplementary files match statement wording
+- data citations appear in the reference list where the journal expects them
+- no claim depends on unavailable data without explanation
+
+## Source notes
+
+- Springer Nature research data policy requires Data Availability statements for original articles
+  and asks authors to describe available data, location, and access terms.
+- Nature Portfolio reporting standards require prompt availability of data, materials, code, and
+  associated protocols, with restrictions disclosed to editors at submission.
+- Scientific Data policy favours repository deposition, especially for primary data, and requires
+  repository hosting for Data Descriptor datasets.

package/src/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

package/src/skills/nature-data/references/source-basis.md

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+# Source Basis
+
+Use this file when a user asks why a rule exists, wants primary-source justification, or needs to
+audit the `nature-data` skill against real policy sources.
+
+## Source map
+
+| Skill rule | Primary support |
+|---|---|
+| Original research needs a Data Availability statement. | Springer Nature research data policy says original articles must include a data availability statement and that it should describe available data, location, and access terms. |
+| The statement must cover original and reused data, including data that cannot be public. | Springer Nature policy applies to datasets needed to interpret and replicate conclusions and explicitly includes original/reused data and non-publicly shareable data. |
+| Supporting data should be public where possible, with mandatory community repositories for some data types. | Springer Nature policy strongly encourages public availability for datasets supporting analysis and conclusions and mandates sharing for community-endorsed data types. |
+| Reviewers may need access to underlying data and code. | Springer Nature policy states peer reviewers are entitled to request access to underlying data and code when needed for evaluation. |
+| Nature-style statements must expose the minimum dataset needed to interpret, verify, and extend the work. | Nature Portfolio reporting standards describe transparent access conditions for the minimum dataset needed to interpret, verify, and extend research. |
+| Materials, data, code, and protocols should be available without undue qualifications, and restrictions must be disclosed. | Nature Portfolio reporting standards state availability is a publication condition and restrictions must be disclosed at submission and in the manuscript. |
+| Repositories are preferred over large supplementary files. | Nature Portfolio reporting standards discourage large datasets in supplementary information and prefer repositories; Scientific Data also strongly encourages repository deposition, especially for primary data. |
+| Repository choice should prefer discipline-specific, community-recognised repositories, with generalist or institutional repositories as fallback. | Springer Nature repository guidance recommends discipline-specific community repositories where possible, otherwise generalist or institutional repositories. |
+| Sensitive data should use safe sharing, controlled access, metadata records, or trusted environments where appropriate. | Springer Nature sensitive data guidance recommends repository use where possible, controlled-access repositories, trusted research environments, and metadata records for non-public data. |
+| Human, non-human sensitive, proprietary, and third-party data need explicit rights and access logic. | Springer Nature sensitive data guidance lists identifiable human data, other sensitive data, and proprietary/third-party data as categories requiring special handling. |
+| Rawness and reusability should follow community norms. | Scientific Data policy says data should be provided at a level of rawness allowing reuse in line with accepted community norms. |
+| FAIR checks should include findability, accessibility, interoperability, and reusability for humans and machines. | Wilkinson et al. formally describe the FAIR principles and emphasize findable, accessible, interoperable, reusable digital objects for people and machines. |
+| Dataset citation metadata should include persistent identifiers and core descriptive fields. | DataCite Metadata Schema defines core metadata properties for accurate and consistent identification, citation, and retrieval of resources. |
+
+## Official sources
+
+- Springer Nature, Research data policy:
+  <https://www.springernature.com/gp/journal-policies/15369670>
+- Springer Nature, Data availability statements:
+  <https://www.springernature.com/gp/authors/research-data-policy/data-availability-statements>
+- Springer Nature, Data repository guidance:
+  <https://www.springernature.com/gp/authors/research-data-policy/recommended-repositories>
+- Springer Nature, Sensitive data:
+  <https://www.springernature.com/gp/authors/research-data-policy/sensitive-data>
+- Nature Portfolio, Reporting standards and availability of data, materials, code and protocols:
+  <https://www.nature.com/nature-portfolio/editorial-policies/reporting-standards>
+- Example Nature Portfolio journal reporting standards page:
+  <https://www.nature.com/npj2dmaterials/editorial-policies/reporting-standards>
+- Nature Research, Data availability statements and data citations policy FAQ:
+  <https://www.nature.com/documents/nr-data-availability-statements-data-citations-faqs.pdf>
+- Scientific Data, Data policies:
+  <https://www.nature.com/sdata/policies/data-policies>
+- Wilkinson et al. 2016, The FAIR Guiding Principles for scientific data management and stewardship:
+  <https://www.nature.com/articles/sdata201618>
+- DataCite Metadata Schema:
+  <https://schema.datacite.org/>
+
+## Notes for future updates
+
+- Check target journal instructions first because Nature Portfolio journals can add field-specific
+  requirements.
+- Check DataCite's latest schema before naming version-specific fields. As of 2026-05-01, the
+  DataCite schema landing page lists Metadata Schema 4.7 as the latest release.
+- Keep this file as a source map, not a long policy mirror. Link to official pages rather than
+  copying full policy text.

package/src/skills/nature-data/references/statement-patterns.md

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+# Statement Patterns
+
+Use these patterns as starting points. Replace bracketed fields with verified information. Delete
+any sentence that does not apply.
+
+For Chinese users, treat the Chinese line under each pattern as author-facing guidance, not as
+submission text. Submit the English statement unless the journal explicitly asks otherwise.
+
+## Public repository, single dataset
+
+```text
+The [raw/processed/source] data supporting the findings of this study are available in
+[Repository] under accession [ACCESSION] / at [DOI or persistent URL]. The deposited record
+contains [brief contents: e.g. raw measurements, processed tables, figure source data, metadata
+and analysis inputs].
+```
+
+中文对应：本研究的原始/处理后/源数据已存储在某个正式仓库，并有登录号、DOI 或永久链接。
+
+## Public repository, multiple datasets
+
+```text
+The datasets generated in this study are available as follows: [dataset family 1] in
+[Repository] under [DOI/accession]; [dataset family 2] in [Repository] under [DOI/accession];
+and figure source data in [Repository/Supplementary Data file] under [identifier or file name].
+```
+
+中文对应：不同类型数据分别放在不同仓库或文件中，需要逐一说明，不能笼统写“数据见附件”。
+
+## Data in paper and supplementary files only
+
+Use only when the supporting dataset is genuinely small and fully represented in the article,
+source data, or supplementary files.
+
+```text
+All data supporting the findings of this study are included in the paper, its Supplementary
+Information, and Source Data files. [Name exact Supplementary Tables/Data files when possible.]
+```
+
+中文对应：只有当支撑结论的数据确实都在正文、补充材料和 Source Data 中时才这样写。
+
+## Reused public data
+
+```text
+This study used publicly available [dataset name/type] from [Repository or source], available under
+[DOI/accession/stable URL]. We used [version/release/date accessed, if relevant]. No new primary
+[data type] data were generated for this part of the analysis.
+```
+
+中文对应：使用公开数据库时，需要写清数据库名、版本/发布日期/访问日期和编号，并引用数据集。
+
+## Mixed generated and reused data
+
+```text
+Data generated in this study are available in [Repository] under [DOI/accession]. Public datasets
+reused in the analysis were obtained from [source 1, identifier/version] and [source 2,
+identifier/version]. Source data for [figures/tables] are provided in [location].
+```
+
+中文对应：自己产生的数据和复用的公开数据要分开写，避免让读者误以为所有数据都是本研究产生。
+
+## Controlled-access human or sensitive data
+
+```text
+The [data type] data supporting this study are not publicly available because [privacy, consent,
+legal, ethical or security reason]. A metadata record is available at [repository/accession, if
+available]. Qualified researchers may request access from [data access committee/institutional
+office/repository procedure] at [contact or URL]. Access requires [ethics approval/data-use
+agreement/other conditions] and will be reviewed according to [policy or committee name].
+```
+
+中文对应：涉及人类参与者、隐私或伦理限制时，不能只写“因隐私不可公开”；还要写申请路径和审核条件。
+
+## Third-party or licensed data
+
+```text
+The [data type/name] data used in this study were obtained from [third-party provider] under
+licence and are not publicly redistributable by the authors. Requests for access should be directed
+to [provider/contact/URL]. Derived data that can be shared are available in [repository] under
+[DOI/accession], subject to [licence or restriction].
+```
+
+中文对应：第三方授权数据不能由作者重新分发时，要说明数据所有者和读者应向谁申请。
+
+## Commercially restricted data
+
+```text
+The [data type] data are subject to commercial restrictions and cannot be made publicly available.
+Requests for access may be directed to [company/data owner/contact or URL] and are subject to
+[approval/licence/payment/confidentiality terms]. The authors provide [summary statistics,
+metadata, synthetic data, or source data] in [location] to support interpretation of the results.
+```
+
+中文对应：企业或商业数据不可公开时，需要说明商业限制、申请对象，以及是否有汇总数据或元数据可公开。
+
+## Embargoed data
+
+Use only when the repository supports embargo and the journal permits it.
+
+```text
+The [data type] data have been deposited in [Repository] under [DOI/accession] and are under
+embargo until [date/event]. Reviewers can access the data using [private reviewer link or
+repository access route]. The data will become publicly available at [DOI/accession] when the
+embargo ends.
+```
+
+中文对应：如果数据暂时不公开，必须已有仓库记录、审稿访问方式和明确解封时间或条件。
+
+## Request-based access with justified restriction
+
+```text
+The [data type] data are not publicly available because [specific reason]. Requests for access may
+be sent to [institutional group/contact route], and will be considered for [eligible purpose/users]
+subject to [approval, agreement, or legal condition]. [Public metadata/aggregate data/source data]
+are available at [location].
+```
+
+中文对应：“合理请求”只有在说明原因、接收机构、审核条件和可公开元数据后才可接受。
+
+## No datasets generated or analysed
+
+Use sparingly.
+
+```text
+No datasets were generated or analysed during the current study.
+```
+
+中文对应：只有确实没有生成或分析任何数据时才能使用，经验研究通常不适用。
+
+For theory papers, be more specific:
+
+```text
+This work is theoretical and does not generate or analyse empirical datasets.
+```
+
+## Anti-patterns to revise
+
+| Weak wording | Why it fails | Stronger move |
+|---|---|---|
+| Data are available upon request. | No reason, route, eligibility, or durability. | Add restriction reason, responsible access body, conditions, and metadata. |
+| Data are available from the corresponding author on reasonable request. | Often a literal translation of "可向通讯作者合理索取"; not durable or specific enough. | Use an institutional/repository access route and define review conditions. |
+| Data will be uploaded after acceptance. | No current repository or durable identifier. | Deposit before submission or provide a private reviewer link. |
+| All data are in the manuscript. | Often false for figures/statistics. | Name exact source data, supplementary files, and omitted raw data. |
+| Data are proprietary. | Does not say who controls access. | Name owner/provider and access route. |
+| N/A. | Nature-style instructions usually require an explanation. | State why no datasets were generated or analysed. |
+
+## Audit questions
+
+- Which result would fail if this dataset were unavailable?
+- Is the route durable beyond the corresponding author's current email address?
+- Can a reader tell what each identifier contains?
+- Are restrictions specific enough for an editor to judge them?
+- Are reused datasets cited, not merely mentioned?