Europe PMC MCP Server

A Model Context Protocol (MCP) server for Europe PMC — open-access biomedical literature: search across 45M+ abstracts, retrieve OA full-text (JATS XML), text-mined annotations, citations/references, and database cross-links. One of 100+ servers in the Bio MCP monorepo.

Connect

https://europepmc-mcp-server.quentincody.workers.dev/mcp

Local dev runs at http://localhost:8904/mcp (./scripts/dev-servers.sh europepmc).

Tools

• europepmc_search — discover endpoints (Code Mode catalog search)
• europepmc_execute — Code Mode: api.get(...) in a V8 isolate across two upstreams (Articles + Annotations APIs)
• europepmc_query_data — SQL over large responses auto-staged into per-session SQLite
• europepmc_get_schema — inspect a staged dataset's schema

Wraps two upstream bases in one isolate (routed in api-adapter.ts): the Articles RESTful API (/search, /{PMCID}/fullTextXML, /{source}/{id}/citations|references|databaseLinks) and the Annotations API (/annotations/annotationsByArticleIds|annotationsByEntity). Every _execute result carries a _meta.citation (Europe PMC / EMBL-EBI).

Key usage notes (also in the catalog notes): pagination is cursorMark (start *, thread nextCursorMark; the page param is ignored); format=json is injected automatically; full text is XML-only and auto-staged; metadata/abstracts are open + commercial-OK, but per-article full-text licenses are mixed (CC-BY vs CC-BY-NC/-ND) — gate any caching/redistribution on the per-article license field (present in resultType=core).

Architecture / maintenance

• Archetype: catalog-only REST + Code Mode (dual upstream). No auth. Rate limit ~10 req/s per IP, shared across Cloudflare egress → be gentle.
• Drift risk: low. Refresh cadence: quarterly catalog review. Known gaps: supplementaryFiles (binary ZIP) not exposed in v1; standalone textMinedTerms/fullTextUrlList are 404 upstream (use the Annotations API / the core result's inline fields).

Development

./scripts/dev-servers.sh europepmc
pnpm --filter europepmc-mcp-server run deploy

See docs/adding-mcp-servers.md and the build plan docs/plans/2026-06-26-evidence-genomics-mcp-servers.md.