@cyanheads/pubmed-mcp-server/dist/index.js

Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.

#!/usr/bin/env node
/**
 * @fileoverview PubMed MCP server entry point.
 * @module index
 */
import { createApp } from '@cyanheads/mcp-ts-core';
import { getServerConfig } from './config/server-config.js';
import { researchPlanPrompt } from './mcp-server/prompts/definitions/research-plan.prompt.js';
import { databaseInfoResource } from './mcp-server/resources/definitions/database-info.resource.js';
import { convertIdsTool } from './mcp-server/tools/definitions/convert-ids.tool.js';
import { fetchArticlesTool } from './mcp-server/tools/definitions/fetch-articles.tool.js';
import { fetchFulltextTool } from './mcp-server/tools/definitions/fetch-fulltext.tool.js';
import { findRelatedTool } from './mcp-server/tools/definitions/find-related.tool.js';
import { formatCitationsTool } from './mcp-server/tools/definitions/format-citations.tool.js';
import { lookupCitationTool } from './mcp-server/tools/definitions/lookup-citation.tool.js';
import { lookupMeshTool } from './mcp-server/tools/definitions/lookup-mesh.tool.js';
import { pubmedEuropepmcSearchTool } from './mcp-server/tools/definitions/pubmed-europepmc-search.tool.js';
import { searchArticlesTool } from './mcp-server/tools/definitions/search-articles.tool.js';
import { spellCheckTool } from './mcp-server/tools/definitions/spell-check.tool.js';
import { initEuropePmcService } from './services/europe-pmc/europe-pmc-service.js';
import { initNcbiService } from './services/ncbi/ncbi-service.js';
import { initUnpaywallService } from './services/unpaywall/unpaywall-service.js';
const config = getServerConfig();
const tools = [
    searchArticlesTool,
    fetchArticlesTool,
    fetchFulltextTool,
    formatCitationsTool,
    findRelatedTool,
    spellCheckTool,
    lookupMeshTool,
    lookupCitationTool,
    convertIdsTool,
    ...(config.europepmcEnabled ? [pubmedEuropepmcSearchTool] : []),
];
await createApp({
    tools,
    resources: [databaseInfoResource],
    prompts: [researchPlanPrompt],
    instructions: "Use the pubmed_* tools to search PubMed and PubMed Central, fetch article metadata and full text, format citations, and find related articles via NCBI's E-utilities. Articles are keyed by PMID (integer); PMC full text by PMCID (`PMC` prefix); most also carry a DOI. Typical flow: `pubmed_search_articles` → `pubmed_fetch_articles` → `pubmed_fetch_fulltext`. When PubMed itself comes up empty (preprints, EPMC-only OA), broaden via `pubmed_europepmc_search`. Prefer deterministic resolvers when inputs are structured: `pubmed_lookup_citation` for partial references, `pubmed_convert_ids` to crosswalk IDs. Refine queries with `pubmed_lookup_mesh` and `pubmed_spell_check`.",
    landing: {
        tagline: 'Search PubMed, fetch articles, generate citations, explore MeSH terms, and discover related research.',
        repoRoot: 'https://github.com/cyanheads/pubmed-mcp-server',
        links: [
            { label: 'PubMed', href: 'https://pubmed.ncbi.nlm.nih.gov/', external: true },
            {
                label: 'E-utilities docs',
                href: 'https://www.ncbi.nlm.nih.gov/books/NBK25501/',
                external: true,
            },
            {
                label: 'Get an NCBI API key',
                href: 'https://www.ncbi.nlm.nih.gov/account/settings/',
                external: true,
            },
            { label: 'MeSH Browser', href: 'https://meshb.nlm.nih.gov/', external: true },
        ],
        envExample: {
            NCBI_API_KEY: 'your-ncbi-api-key',
            NCBI_ADMIN_EMAIL: 'you@example.com',
            UNPAYWALL_EMAIL: 'you@example.com',
        },
    },
    setup() {
        initNcbiService();
        initUnpaywallService();
        initEuropePmcService();
    },
});
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