pvliesdonk-scholar-mcp 1.6.0

FastMCP server for Semantic Scholar with OpenAlex enrichment and docling PDF conversion

scholar-mcp

A FastMCP server providing structured academic literature access via Semantic Scholar, with OpenAlex enrichment and optional docling-serve PDF conversion.

Features

• Search & retrieval -- full-text paper search with year, venue, field-of-study, and citation-count filters; single-paper lookup by DOI, S2 ID, arXiv ID, and more; author profile and name search
• Citation graph -- forward citations, backward references, BFS graph traversal up to configurable depth, and shortest-path bridge paper discovery
• Recommendations -- paper recommendations from positive (and optional negative) examples via the S2 recommendation API
• Citation generation -- format paper metadata as BibTeX, CSL-JSON, or RIS citations with automatic entry type inference, author name parsing, and OpenAlex venue enrichment
• Book search -- search and fetch book metadata via Open Library (no API key required); papers with an ISBN are automatically enriched with publisher, edition, cover URL, and subject data
• OpenAlex enrichment -- augment paper metadata with open-access URLs, affiliations, funders, concepts, and OA status
• Patent search & cross-referencing -- search and retrieve patents via EPO Open Patent Services covering 100+ patent offices, with cited reference extraction, NPL-to-paper resolution via Semantic Scholar, and paper-to-patent citation discovery; EPO credentials are optional -- paper search works without them
• PDF conversion -- download open-access PDFs and convert to Markdown via docling-serve, with optional VLM enrichment for formulas and figures; automatic fallback to ArXiv, PubMed Central, and Unpaywall when Semantic Scholar has no OA link; direct URL download for PDFs found elsewhere
• Intelligent caching -- SQLite-backed cache with per-table TTLs (30 days for papers/authors, 7 days for citations/references) and identifier aliasing
• Authentication -- bearer token, OIDC (OAuth 2.1), or both simultaneously (multi-auth)
• Multi-transport -- stdio (Claude Desktop), HTTP (streamable-http), and SSE transports
• Linux packages -- .deb and .rpm packages with systemd service and security hardening

Installation

With uvx (recommended)

uvx --from pvliesdonk-scholar-mcp scholar-mcp serve

With pip

pip install 'pvliesdonk-scholar-mcp[mcp]'
scholar-mcp serve

With Docker

docker run -v scholar-mcp-data:/data/scholar-mcp \
           ghcr.io/pvliesdonk/scholar-mcp:latest

Linux packages

Download .deb or .rpm from the latest release:

# Debian/Ubuntu
sudo dpkg -i scholar-mcp_*.deb

# RHEL/Fedora
sudo rpm -i scholar-mcp-*.rpm

Note: The PyPI package is pvliesdonk-scholar-mcp. The CLI command installed is scholar-mcp.

Quick Start

stdio transport (Claude Desktop / MCP clients)

uvx --from pvliesdonk-scholar-mcp scholar-mcp serve

API key optional but recommended: The server works without a Semantic Scholar API key, but unauthenticated requests are limited to ~1 req/s and will hit 429 throttles quickly during multi-step operations like citation graph traversal. Request a free key to get ~10 req/s.

Claude Desktop configuration (claude_desktop_config.json):

{
  "mcpServers": {
    "scholar": {
      "command": "uvx",
      "args": ["--from", "pvliesdonk-scholar-mcp", "scholar-mcp", "serve"],
      "env": {
        "SCHOLAR_MCP_S2_API_KEY": "your-key"
      }
    }
  }
}

HTTP transport

uvx --from pvliesdonk-scholar-mcp scholar-mcp serve --transport http --port 8000

Configuration

All settings are controlled via environment variables with the SCHOLAR_MCP_ prefix.

Core

Variable	Default	Description
SCHOLAR_MCP_S2_API_KEY	--	Semantic Scholar API key (request one); optional but recommended for higher rate limits
SCHOLAR_MCP_READ_ONLY	true	If true, write-tagged tools (fetch_paper_pdf, convert_pdf_to_markdown, fetch_and_convert, fetch_pdf_by_url) are hidden
SCHOLAR_MCP_CACHE_DIR	/data/scholar-mcp	Directory for the SQLite cache database and downloaded PDFs
SCHOLAR_MCP_CONTACT_EMAIL	--	Included in the OpenAlex User-Agent for polite pool access (faster rate limits); also enables Unpaywall PDF lookups
SCHOLAR_MCP_LOG_LEVEL	INFO	Logging level (DEBUG, INFO, WARNING, ERROR)

PDF Conversion (optional)

Variable	Default	Description
SCHOLAR_MCP_DOCLING_URL	--	Base URL of a running docling-serve instance (e.g. http://localhost:5001)
SCHOLAR_MCP_VLM_API_URL	--	OpenAI-compatible VLM endpoint for formula/figure-enriched PDF conversion
SCHOLAR_MCP_VLM_API_KEY	--	API key for the VLM endpoint
SCHOLAR_MCP_VLM_MODEL	gpt-4o	Model name for VLM-enriched conversion

Patent Search (optional)

Variable	Default	Description
SCHOLAR_MCP_EPO_CONSUMER_KEY	--	EPO OPS consumer key (register at developers.epo.org); both key and secret must be set for patent tools to appear
SCHOLAR_MCP_EPO_CONSUMER_SECRET	--	EPO OPS consumer secret

Authentication (optional)

Variable	Default	Description
SCHOLAR_MCP_BEARER_TOKEN	--	Static bearer token for HTTP transport authentication
SCHOLAR_MCP_BASE_URL	--	Public base URL, required for OIDC (e.g. https://mcp.example.com)
SCHOLAR_MCP_OIDC_CONFIG_URL	--	OIDC discovery endpoint URL
SCHOLAR_MCP_OIDC_CLIENT_ID	--	OIDC client ID
SCHOLAR_MCP_OIDC_CLIENT_SECRET	--	OIDC client secret
SCHOLAR_MCP_OIDC_JWT_SIGNING_KEY	--	JWT signing key; required on Linux/Docker to survive restarts (openssl rand -hex 32)

MCP Tools

Search & Retrieval

Tool	Description
search_papers	Full-text search with year, venue, field-of-study, and citation-count filters. Returns up to 100 results with pagination.
get_paper	Fetch full metadata for a single paper by DOI, S2 ID, arXiv ID, ACM ID, or PubMed ID.
get_author	Fetch author profile with publications, or search by name.

Citation Graph

Tool	Description
get_citations	Forward citations (papers that cite a given paper) with optional filters.
get_references	Backward references (papers cited by a given paper).
get_citation_graph	BFS traversal from seed papers, returning nodes + edges up to configurable depth.
find_bridge_papers	Shortest citation path between two papers.

Recommendations

Tool	Description
recommend_papers	Paper recommendations from 1--5 positive examples and optional negative examples.

Book Search

Tool	Description
search_books	Search for books by title, author, ISBN, or keywords via Open Library. Returns up to 50 results.
get_book	Fetch book metadata by ISBN-10, ISBN-13, Open Library work ID (OL...W), or edition ID (OL...M).
recommend_books	Recommend books for a subject via Open Library, sorted by popularity.

Papers with an ISBN in their externalIds are automatically enriched with book_metadata (publisher, edition, cover URL, subjects, and more) from Open Library when fetched via get_paper, get_citations, get_references, or get_citation_graph.

Utility

Tool	Description
batch_resolve	Resolve up to 100 identifiers to full metadata in one call, with OpenAlex fallback.
enrich_paper	Augment S2 metadata with OpenAlex fields (affiliations, funders, OA status, concepts).

Citation Generation

Tool	Description
generate_citations	Generate BibTeX, CSL-JSON, or RIS citations for up to 100 papers, with automatic entry type inference and optional OpenAlex venue enrichment.

Patent Search (requires EPO OPS credentials)

Tool	Description
search_patents	Search patents across 100+ patent offices via EPO OPS.
get_patent	Fetch bibliographic metadata for a single patent by publication number.

Patent tools are hidden when SCHOLAR_MCP_EPO_CONSUMER_KEY and SCHOLAR_MCP_EPO_CONSUMER_SECRET are not set.

PDF Conversion (requires docling-serve)

Tool	Description
fetch_paper_pdf	Download PDF for a paper (S2 open-access, then ArXiv/PMC/Unpaywall fallback).
convert_pdf_to_markdown	Convert a local PDF to Markdown via docling-serve.
fetch_and_convert	Full pipeline: fetch PDF (with fallback), convert to Markdown, return both.
fetch_pdf_by_url	Download a PDF from any URL and optionally convert to Markdown.

PDF tools are write-tagged and hidden when SCHOLAR_MCP_READ_ONLY=true (the default).

Task Polling

Tool	Description
get_task_result	Poll for the result of a background task by ID.
list_tasks	List all active background tasks.

Long-running operations (PDF download/conversion) and rate-limited S2 requests return {"queued": true, "task_id": "..."} immediately. Use get_task_result to poll for the result.

Docker Compose

services:
  scholar-mcp:
    image: ghcr.io/pvliesdonk/scholar-mcp:latest
    restart: unless-stopped
    environment:
      SCHOLAR_MCP_S2_API_KEY: "${SCHOLAR_MCP_S2_API_KEY}"
      SCHOLAR_MCP_DOCLING_URL: "http://docling-serve:5001"
      SCHOLAR_MCP_VLM_API_URL: "${VLM_API_URL:-}"
      SCHOLAR_MCP_VLM_API_KEY: "${VLM_API_KEY:-}"
      SCHOLAR_MCP_CACHE_DIR: "/data/scholar-mcp"
      SCHOLAR_MCP_READ_ONLY: "false"
    volumes:
      - scholar-mcp-data:/data/scholar-mcp
    labels:
      - "traefik.enable=true"
      - "traefik.http.routers.scholar-mcp.rule=Host(`scholar-mcp.yourdomain.com`)"

  docling-serve:
    image: ghcr.io/ds4sd/docling-serve:latest
    restart: unless-stopped

volumes:
  scholar-mcp-data:

Cache Management

# Show cache statistics (row counts, database size)
scholar-mcp cache stats

# Clear all cached data (preserves identifier aliases)
scholar-mcp cache clear

# Remove entries older than 30 days
scholar-mcp cache clear --older-than 30

# Override cache directory
scholar-mcp cache stats --cache-dir /path/to/cache

Development

# Install with dev and MCP dependencies
uv sync --extra dev --extra mcp

# Run tests
uv run pytest

# Lint and format
uv run ruff check src/ tests/
uv run ruff format src/ tests/

# Type check
uv run mypy src/

# Build docs locally
uv sync --extra docs
uv run mkdocs serve

License

MIT