/nature-academic-search

name: nature-academic-search
description: >-
  Multi-source literature search, citation verification, MeSH search strategy,
  citation file management (.nbib/.ris/.bib conversion), and reference management
  (BibTeX, related articles, ID conversion) via MCP tools (PubMed, CrossRef, arXiv).
  Use when the user needs coordinated multi-step literature workflows beyond a
  single MCP call.

Academic Search

Multi-source literature search, citation verification, citation format conversion, and reference management via MCP tools.

MCP Tools

Core Search

| Tool | Source | Best For | |------|--------|----------| | `pubmed_search_articles` | PubMed MCP | Biomedical, MeSH, clinical trials | | `search_crossref` | paper-search MCP | Cross-disciplinary, citation counts | | `search_arxiv` | paper-search MCP | Preprints (physics, math, CS, biology) |

Extended Search

| Tool | Source | Best For | |------|--------|----------| | `search_google_scholar` | paper-search MCP | Broad academic search (scraped) | | `search_semantic_scholar` | paper-search MCP | Citation graph, field-of-study filters | | `search_biorxiv` | paper-search MCP | Biology preprints | | `search_medrxiv` | paper-search MCP | Medical preprints | | `search_webofscience` | paper-search MCP | Curated index, citation reports | | `search_scopus` | paper-search MCP | Broad scholarly database |

PubMed Utilities

| Tool | Purpose | |------|---------| | `pubmed_fetch_articles` | Full metadata by PMID | | `pubmed_find_related` | Related article discovery | | `pubmed_format_citations` | APA / MLA / BibTeX / RIS formatting | | `pubmed_convert_ids` | DOI ↔ PMID ↔ PMCID conversion | | `pubmed_lookup_mesh` | MeSH term exploration and hierarchy | | `pubmed_lookup_citation` | Bibliographic citation → PMID lookup |

Source Routing

See [Source Tiers & Reliability](references/source-tiers.md) for the complete reliability classification and fallback routing rules. The T1→T2→T3 fallback chain is the standard execution order across all workflows.

Quick guide:

| User need | Primary (T1) | Secondary (T2) | Last Resort (T3) | |-----------|-------------|-----------------|-------------------| | Medical / clinical | PubMed | Semantic Scholar | Google Scholar | | Cross-disciplinary | CrossRef | Semantic Scholar | Scopus | | Preprints / CS / physics | arXiv | bioRxiv / medRxiv | — | | Exhaustive review | PubMed + CrossRef + arXiv | Semantic Scholar + bioRxiv/medRxiv | WoS / Scopus | | Citation count sensitive | Semantic Scholar | CrossRef | — | | Chinese literature | — | — | CNKI / 万方 (manual) |

Workflows

| # | Workflow | Reference | |---|----------|-----------| | 1 | Multi-Source Literature Search | [wf1](references/workflows/wf1-multi-source-search.md) | | 2 | Citation Verification | [wf2](references/workflows/wf2-citation-verification.md) | | 3 | MeSH Search Strategy | [wf3](references/workflows/wf3-mesh-strategy.md) | | 4 | Citation File Management | [wf4](references/workflows/wf4-citation-file-mgmt.md) | | 5 | Reference Management | [wf5](references/workflows/wf5-reference-mgmt.md) |

Shared Modules

| Module | Purpose | |--------|---------| | [Dedup Engine](references/dedup-engine.md) | Unified deduplication (WFs 1, 2, 5a) | | [Citation Parser](references/citation-parser.md) | Extract citations from documents (WF 2) | | [Search Strategy](references/search-strategy.md) | Query construction, source selection, ranking | | [RIS/BibTeX Format](references/ris-bibtex-format.md) | Format specifications and field mappings | | [Format Converter](scripts/format-converter.py) | Multi-source .nbib/.ris/.bib downloader |

Environment Setup

API Keys (optional but recommended)

| Service | Env Var | Register At | Free Tier | |---------|---------|-------------|-----------| | Semantic Scholar | `SEMANTIC_SCHOLAR_API_KEY` | [api.semanticscholar.org](https://api.semanticscholar.org/) | 100 req/s with key (1/s without) | | NCBI E-utilities | `NCBI_API_KEY` | [ncbi.nlm.nih.gov/account](https://www.ncbi.nlm.nih.gov/account/) | 10 req/s with key (3/s without) |

Set via `export` or `.env` file.

Proxy (if behind firewall)

export http_proxy=http://127.0.0.1:7890
export https_proxy=http://127.0.0.1:7890

Pre-flight Check

python scripts/preflight.py

Run before batch operations to verify API endpoints are reachable.

Format Converter Dependencies

The format converter (`scripts/format-converter.py`) uses Python stdlib only — no extra dependencies. Run `python scripts/format-converter.py --test` to verify the conversion pipeline.

Error Handling

• **MCP tool unavailable**: report specific failure, continue with remaining tools.
• **No results**: broaden terms, try alternative sources, suggest user refine query.
• **Script failure (2x)**: fall back to manual generation from MCP-fetched metadata.

Limitations

• Google Scholar and Semantic Scholar are scraped (not API-backed) — results may vary.
• Chinese literature (CNKI / 万方) not indexed by CrossRef or PubMed.
• Citation counts may be delayed (CrossRef updates monthly).