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).