nature-academic-search

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 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

Module	Purpose
Dedup Engine	Unified deduplication (WFs 1, 2, 5a)
Citation Parser	Extract citations from documents (WF 2)
Search Strategy	Query construction, source selection, ranking
RIS/BibTeX Format	Format specifications and field mappings
Format Converter	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	100 req/s with key (1/s without)
NCBI E-utilities	NCBI_API_KEY	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).