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nature-academic-search

Search academic literature across sources, verify references, and convert citation files. Build PubMed queries using MeSH, its subject vocabulary, or audit citations to distinguish independent citations and document who cited a paper and how.

OriginalShow the original 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.

Run score Not tested

See how to install

Good for

  • Search academic literature across multiple sources
  • Verify references extracted from a document
  • Build a MeSH-based PubMed search strategy
  • Convert and organize citation files
  • Audit independent citations and citing researchers

Overview

What it does

nature-academic-search supports academic literature searches across multiple sources, citation checks, and reference-file organization. It can check citation details extracted from a document, find related papers, and convert literature identifiers. It also helps design PubMed search queries using MeSH, PubMed’s subject vocabulary, and audit citations while distinguishing independent citations from self-citations. The results can organize who cited a paper and the context in which it was cited, with supporting evidence.

When it helps

Use it to search prior work across more than one source, check the references in a manuscript, or manage .nbib, .ris, and .bib files. It can also organize citation measures for individual papers and investigate the background or positions of people who cited them.

Example requests

  • “Search multiple sources for literature on this topic and organize the references.”
  • “Check the citation details in this document.”
  • “Find independent citations to this paper and examine the contexts in which it was cited.”

Notes

Search and verification may require MCP tools or API settings for the sources used, as well as network access. Converting supplied, complete citation records is intended to work offline. Paper translation and drafting manuscript text are outside the skill’s scope.

This overview was written by AI (OpenAI Codex) from the public SKILL.md. Check the original below for the exact behavior.

Document check

AI checked the SKILL.md for operations that need care and for setup requirements. The score comes only from actually running the skill (hands-on test).

SafetyAre sending data, deleting files, and running commands disclosed?
BPartly lackingRetrieval uses network and API settings; credential handling is unstated.
Easy setupDoes it need few tools or API keys, and are they documented?
BPartly lackingRetrieval may need MCP tools or API setup, with details unspecified.

Not counted in the score. Rated by AI (OpenAI Codex) as of Oct 24, 2026. Treat it as a guide and read the original before installing.

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Files included (54)

  • SKILL.md3.5 KB
  • agents/openai.yaml265 B
  • config/mcp-snippet.json502 B
  • config/settings-snippet.json59 B
  • config/triggers-academic-search.toml978 B
  • install.sh4.3 KB
  • manifest.yaml3.1 KB
  • mcp-server/academic_search_server.py20.9 KB
  • mcp-server/config.toml249 B
  • mcp-server/README.md1.9 KB
  • mcp-server/requirements.txt134 B
  • mcp-server/sources/__init__.py352 B
  • mcp-server/sources/arxiv.py11.4 KB
  • mcp-server/sources/crossref.py6.9 KB
  • mcp-server/sources/elsevier_common.py2.4 KB
  • mcp-server/sources/pubmed.py13.1 KB
  • mcp-server/sources/sciencedirect.py6.9 KB
  • mcp-server/sources/scopus.py19.0 KB
  • mcp-server/tests/__init__.py40 B
  • mcp-server/tests/test_arxiv_error_entries.py1.4 KB
  • mcp-server/tests/test_citation_errors.py1.6 KB
  • mcp-server/tests/test_elsevier_live.py2.6 KB
  • mcp-server/tests/test_format_converter_hardening.py4.2 KB
  • mcp-server/tests/test_mcp_tools.py2.6 KB
  • mcp-server/tests/test_pubmed_parsing.py894 B
  • mcp-server/tests/test_scopus_empty_result.py1006 B
  • mcp-server/tests/test_script_converters.py2.9 KB
  • mcp-server/tests/test_sources.py30.5 KB
  • mcp-server/utils/__init__.py359 B
  • mcp-server/utils/config.py1.4 KB
  • mcp-server/utils/errors.py620 B
  • mcp-server/utils/logging.py1.1 KB
  • README_EN.md2.7 KB
  • README.md2.4 KB
  • references/citation-parser.md2.7 KB
  • references/dedup-engine.md1.9 KB
  • references/pubmed-28344011.bib3.3 KB
  • references/pubmed-28344011.nbib11.9 KB
  • references/pubmed-28344011.ris3.4 KB
  • references/ris-bibtex-format.md4.5 KB
  • references/search-strategy.md2.0 KB
  • references/source-tiers.md2.7 KB
  • references/workflows/wf1-multi-source-search.md1.9 KB
  • references/workflows/wf2-citation-verification.md1.6 KB
  • references/workflows/wf3-mesh-strategy.md538 B
  • references/workflows/wf4-citation-file-mgmt.md1.9 KB
  • references/workflows/wf5-reference-mgmt.md1.3 KB
  • references/workflows/wf6-strict-other-citation-impact-audit.md11.0 KB
  • scripts/academic_search.py20.4 KB
  • scripts/converters.py18.5 KB
  • scripts/format-converter.py19.5 KB
  • scripts/preflight.py3.7 KB
  • static/core/routing-and-ops.md5.0 KB
  • static/core/tools.md3.0 KB

SKILL.md (original)

Review the instructions the agent will receive before you install.

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.

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