pvliesdonk-scholar-mcp 1.8.1

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

scholar-mcp

A FastMCP server for the scholarly citation landscape -- papers, patents, books, and standards -- giving LLMs a unified way to search, cross-reference, and retrieve prior art across all four source types via Semantic Scholar, EPO Open Patent Services, Open Library, and standards bodies (NIST, IETF, W3C, ETSI), with OpenAlex enrichment and optional docling-serve PDF/full-text conversion.

Features

Source domains

• Papers -- full-text search with year/venue/field/citation filters; single-paper lookup by DOI, S2 ID, arXiv ID, ACM ID, or PubMed ID; author profile and name search; forward citations, backward references, BFS graph traversal, shortest-path bridge discovery; recommendations from positive/negative examples; BibTeX/CSL-JSON/RIS citation generation with OpenAlex venue enrichment.
• Patents -- search across 100+ patent offices via EPO OPS with CPC/applicant/inventor/jurisdiction filters; bibliographic, claims, description, family, legal, and citations sections; NPL-to-paper resolution via Semantic Scholar and paper-to-patent citation discovery. EPO credentials are optional -- other domains work without them.
• Books -- search by title/author/keywords via Open Library (no API key required); lookup by ISBN-10/13, Open Library work ID, or edition ID; subject-based recommendations sorted by popularity; Google Books excerpts and preview links; WorldCat permalinks for library discovery; cover image caching. Papers with an ISBN in externalIds are automatically enriched with publisher, edition, cover URL, and subject data from Open Library.
• Standards -- identifier resolution, search, and metadata retrieval for NIST, IETF, W3C, and ETSI standards, with optional full-text fetch and Markdown conversion via docling. Tier 2 ISO, IEC, IEEE, Common Criteria (CC), and CEN/CENELEC metadata (including ISO/IEC/IEEE joint standards and the CC ↔ ISO/IEC 15408 cross-link) is synced locally via sync-standards. ISO, IEC, IEEE have a live-fetch fallback for unsynced identifiers; CC and CEN have no live API and require a sync first. Citations matching standards patterns (RFC, ISO, NIST SP, IEEE, EN, CC) are automatically enriched with structured standard_metadata including identifier, title, body, status, and full-text URL when available (see docs/guides/standards.md).

Cross-cutting

• Enrichment pipeline -- phased enrichment from multiple sources: OpenAlex (OA status, affiliations, funders, concepts), CrossRef (publisher, page ranges, container titles), Google Books (preview links, excerpts), and Open Library (book metadata). Runs automatically on paper and book results.
• 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.

Coverage by domain

Per-domain depth is uneven. Papers currently have the richest tool surface (citation graph, recommendations, cross-referencing to all three other domains); standards are the leanest. That reflects public data availability, not a value hierarchy — writing a paper typically needs all four source types for citations and prior art. Parity work is tracked in GitHub issues and milestones; the roadmap shows intent, not a completeness commitment.

Installation

Claude Code plugin

/plugin marketplace add pvliesdonk/claude-plugins
/plugin install scholar-mcp@pvliesdonk

Claude Desktop (.mcpb bundle)

Download scholar-mcp-<VERSION>.mcpb from the latest release and open it in Claude Desktop, or install via the Claude Desktop MCP gallery.

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

Syncing Tier 2 standards catalogues

Tier 2 bodies (ISO, IEC, IEEE, CC, CEN) are populated from community-curated bulk dumps rather than live-scraped at MCP-server runtime. Run the sync on first install and periodically thereafter:

scholar-mcp sync-standards            # all registered bodies
scholar-mcp sync-standards --body ISO # only ISO
scholar-mcp sync-standards --body IEEE # only IEEE
scholar-mcp sync-standards --body CC   # only Common Criteria
scholar-mcp sync-standards --body CEN # only CEN/CENELEC
scholar-mcp sync-standards --force    # re-sync even if upstream SHA is unchanged

Schedule via cron / launchd / systemd timer — weekly is sufficient; standards change slowly. First sync can take several minutes; subsequent runs that find no upstream changes exit within seconds.

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, fetch_patent_pdf) 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
FASTMCP_LOG_LEVEL	INFO	Logging level (DEBUG, INFO, WARNING, ERROR). Controls all output (app + middleware). The -v CLI flag sets this to DEBUG.
FASTMCP_ENABLE_RICH_LOGGING	true	Set false for plain/JSON-structured log output (e.g. for log aggregators)

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

Google Books (optional)

Variable	Default	Description
SCHOLAR_MCP_GOOGLE_BOOKS_API_KEY	--	Google Books API key for higher rate limits (1000 req/day without key)

Tier 2 standards sync (optional)

Variable	Default	Description
SCHOLAR_GITHUB_TOKEN	--	GitHub personal access token for Relaton sync; lifts unauthenticated GitHub rate limit from 60/hr to 5,000/hr (no scopes required for public-repo reads). Useful for repeated --force testing; daily cron is fine unauthenticated.

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

28 tools, organised by scholarly source type.

Papers

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 & citation generation

Tool	Description
recommend_papers	Paper recommendations from 1--5 positive examples and optional negative examples.
generate_citations	Generate BibTeX, CSL-JSON, or RIS citations for up to 100 papers, with automatic entry type inference and optional OpenAlex venue enrichment.
enrich_paper	Augment Semantic Scholar metadata with OpenAlex fields (affiliations, funders, OA status, concepts).

Patents

Tool	Description
search_patents	Search patents across 100+ patent offices via EPO OPS with CPC / applicant / inventor / jurisdiction / date filters.
get_patent	Fetch bibliographic / claims / description / family / legal / citations sections for a single patent by publication number. Citations include NPL-to-paper resolution via Semantic Scholar.
get_citing_patents	Find patents that cite a given academic paper (best-effort; EPO OPS citation search coverage is incomplete).
fetch_patent_pdf	Download a patent PDF via authenticated EPO OPS and optionally convert to Markdown.

Patent tools are hidden when SCHOLAR_MCP_EPO_CONSUMER_KEY and SCHOLAR_MCP_EPO_CONSUMER_SECRET are not set. fetch_patent_pdf is also write-tagged and hidden when SCHOLAR_MCP_READ_ONLY=true.

Books

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, or edition ID. Optionally download and cache the cover image locally.
get_book_excerpt	Fetch a book excerpt and description from Google Books by ISBN. Shows preview availability and link.
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. Book records also include worldcat_url (when ISBN-13 is present), google_books_url, and snippet from Google Books enrichment. Cover images can be downloaded and cached locally via get_book.

Standards

Tool	Description
resolve_standard_identifier	Normalise a messy citation string (e.g. "rfc9000", "nist 800-53") to canonical form and body.
search_standards	Search standards by identifier, title, or free text, optionally filtered to one body (NIST, IETF, W3C, ETSI).
get_standard	Retrieve a standard by canonical or fuzzy identifier, optionally fetching and converting the full text via docling.

Tier-1 bodies (NIST, IETF, W3C, ETSI) are supported with full metadata and optional full-text conversion. Tier-2 bodies (ISO, IEC, IEEE, CC, CEN/CENELEC) are populated locally via scholar-mcp sync-standards.

Cross-source Utility

Tool	Description
batch_resolve	Resolve up to 100 mixed identifiers (paper DOIs, patent numbers, ISBNs) to full metadata in one call, routing each to the right backend with OpenAlex fallback.

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). fetch_patent_pdf (above) and the get_standard full-text mode cover the patent and standards equivalents.

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 backend 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