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nature-academic-search

yuan1z0825/nature-skills

Search literature, verify citations, and build MeSH strategies for academic research.

What is nature-academic-search?

A routing skill for academic literature discovery across multiple sources, citation verification, and reference management. Use it to search PubMed and other databases, validate citations, construct MeSH search strategies, manage citation files, and audit citation impact—not for manuscript drafting or translation.

  • Search literature across multiple academic sources with fallback routing (T1→T2→T3)
  • Verify and validate citations extracted from documents
  • Build and optimize MeSH/PubMed search strategies
  • Convert and manage citation files (.nbib, .ris, .bib formats)
  • Perform citation-impact audits and identify high-profile citers
  • Discover related articles and convert between citation ID formats

How to install nature-academic-search

npx skills add https://github.com/yuan1z0825/nature-skills --skill nature-academic-search
Prerequisites
  • Node.js and npx installed
  • Access to PubMed API or other configured academic databases (API keys may be required for some sources)
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How to use nature-academic-search

  1. 1.Install the skill using the provided npx command
  2. 2.Load the manifest.yaml to understand available workflows
  3. 3.Identify your task (search, verification, MeSH strategy, file management, or citation audit)
  4. 4.Load the core tools and routing guidance from static/core/
  5. 5.Load the matching workflow fragment for your task
  6. 6.Execute the workflow using the appropriate MCP tools and shared modules
  7. 7.Consult reference files on demand (dedup engine, citation parser, format converter) as needed

Use cases

Good for
  • Systematically search PubMed and other databases for a literature review
  • Verify that citations in a paper are correctly attributed and accessible
  • Develop a precise MeSH search strategy for a clinical or research question
  • Convert a reference list from one format to another for import into a citation manager
  • Audit which high-profile researchers or institutions have cited your work
Who it's for
  • Academic researchers and clinicians conducting literature reviews
  • Graduate students and postdocs managing large reference collections
  • Librarians and information specialists building search strategies
  • Authors preparing manuscripts and verifying citation accuracy

nature-academic-search FAQ

What workflows does this skill support?

Multi-source search, citation verification, MeSH strategy building, citation file management, reference management (BibTeX and ID conversion), and strict citation-impact audits.

Do I need API keys to use this skill?

For local citation-file conversion, no. For source lookup and retrieval, API setup and network access depend on which sources you query; the skill provides environment setup guidance.

Can this skill translate papers or draft manuscript text?

No. This skill is designed for literature discovery, citation management, and verification—not for translation or prose generation.

What citation file formats are supported?

.nbib (PubMed), .ris (RIS), and .bib (BibTeX) formats are supported for conversion and management.

How does the skill handle sources with no results?

It uses a T1→T2→T3 fallback routing chain: if the primary source fails, it tries secondary sources, then tertiary sources. It also broadens search terms when results are empty.

Full instructions (SKILL.md)

Source of truth, from yuan1z0825/nature-skills.


name: nature-academic-search description: "Search literature across sources, verify or manage citations, and build MeSH strategies or citation-impact audits. Use for 文献检索、引文核对、参考文献管理、严格他引 and evidence-backed citer profiles; not for translating a paper or drafting manuscript prose."

Academic Search — Router

Routing protocol

For local citation-file conversion with complete supplied records, load references/workflows/wf4-citation-file-mgmt.md and its format reference directly. Source lookup, API setup, and network preflight apply only when retrieval or verification is needed; do not require them for a requested offline conversion.

For a new task, load the core and matching resources below. Reuse already loaded guidance on follow-ups; load more only when the task needs it.

1. Load the manifest and the core layer

Read manifest.yaml. It declares the workflow axis, the allowed values, and the file paths each value maps to.

Also read every file listed under always_load:

  • static/core/tools.md — the MCP tool inventory (core search, extended search, PubMed utilities) and the shared-module map.
  • static/core/routing-and-ops.md — the T1→T2→T3 source routing quick guide, environment setup, error handling, and limitations.

2. Detect the workflow

Map the user's need to one or more workflow values:

  • multi-source-search — find literature across sources.
  • citation-verification — verify citations extracted from a document.
  • mesh-strategy — build a MeSH/PubMed search strategy.
  • citation-file-mgmt — convert/manage .nbib/.ris/.bib files.
  • reference-mgmt — BibTeX, related-article discovery, ID conversion.
  • strict-other-citation-impact-audit — determine strict independent other-citations, build article-level citation metric tables, identify high-profile citers (academy members, presidents/deans, talent-award holders, fellows, field leaders), and extract how they cited the target paper.

A combined request (for example search then export) may need more than one. State the detected workflow(s) in one short line before proceeding.

3. Load the matching workflow fragment(s)

Read the file mapped for each detected workflow (under references/workflows/). Do not read every workflow. Each workflow file links to the shared modules it needs.

4. Run the workflow using the loaded material

Apply the loaded material in this order:

  1. Core tools and routing (core/tools.md, core/routing-and-ops.md) — which MCP tool for which need, and the T1→T2→T3 fallback chain for source retrieval.
  2. The workflow fragment — its specific steps.
  3. Shared modules and scripts on demand (dedup, citation parser, search strategy, RIS/BibTeX format, format converter).

Report specific tool failures and continue with remaining tools; broaden terms when there are no results; fall back to manual generation from MCP-fetched metadata if a script fails twice.

5. Reach for references only when needed

The files under references/ (and scripts/) are deep references, not defaults. Open them on demand per the references.on_demand table in the manifest — for example references/source-tiers.md for the full reliability classification, references/dedup-engine.md / references/citation-parser.md / references/search-strategy.md / references/ris-bibtex-format.md for the shared modules, and scripts/academic_search.py (no-MCP fallback discovery search) / scripts/format-converter.py / scripts/preflight.py for the tooling.