| 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. |
| argument-hint | [literature search, citation, MeSH, or reference-management request] |
| version | 0.1.0 |
Academic Search
Multi-source literature search, citation verification, citation format conversion,
and reference management via MCP tools.
MCP Tools
Bundled MCP Server (academic-search)
The bundled MCP server provides these tools — use these names when calling the server:
| Tool | Purpose |
|---|
search_papers | Multi-source search across CrossRef, PubMed, arXiv (concurrent) |
get_paper_by_id | Fetch paper by DOI, PMID, or arXiv ID |
get_citation | Formatted citation output (APA, MLA, BibTeX, etc.) |
lookup_mesh | MeSH term exploration and hierarchy |
External MCP Tools (require separate installation)
The following tools are referenced in workflows but require external MCP servers to be installed separately. If unavailable, fall back to the bundled search_papers tool.
| 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 (external only)
| 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 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 |
| 2 | Citation Verification | wf2 |
| 3 | MeSH Search Strategy | wf3 |
| 4 | Citation File Management | wf4 |
| 5 | Reference Management | wf5 |
Shared Modules
Environment Setup
API Keys (optional but recommended)
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).
