NCBI Entrez MCP Server

import { z } from "zod"; import { BaseTool } from "./base.js"; export class PMCIdConverterTool extends BaseTool { register(): void { this.context.server.tool( "pmc_id_converter", "Convert between different PMC article identifiers including PMC IDs, PubMed IDs (PMID), DOIs, and Manuscript IDs (MID). Supports up to 200 IDs per request.", { ids: z .string() .describe("Comma-separated list of IDs to convert (up to 200)"), idtype: z .enum(["pmcid", "pmid", "mid", "doi"]) .optional() .describe("Type of input IDs (auto-detected if not specified)"), versions: z .enum(["yes", "no"]) .default("no") .describe("Show version information"), showaiid: z .enum(["yes", "no"]) .default("no") .describe("Show Article Instance IDs"), format: z .enum(["xml", "json", "csv"]) .default("json") .describe("Output format"), }, async ({ ids, idtype, versions, showaiid, format }) => { try { if (!ids || ids.trim() === "") { throw new Error("IDs parameter cannot be empty"); } // Clean and validate IDs const cleanIds = ids .split(",") .map((id) => id.trim()) .filter((id) => id !== ""); if (cleanIds.length === 0) { throw new Error("No valid IDs provided"); } if (cleanIds.length > 200) { throw new Error("Too many IDs provided (maximum 200)"); } const params = new URLSearchParams({ ids: cleanIds.join(","), versions: versions, showaiid: showaiid, format: format, tool: this.context.defaultTool, email: this.context.defaultEmail, }); if (idtype) { params.append("idtype", idtype); } const url = `https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?${params}`; const response = await fetch(url); const data = await this.parseResponse(response, "PMC ID Converter"); return { content: [ { type: "text", text: `PMC ID Converter Results:\n\n${this.formatResponseData(data)}`, }, ], }; } catch (error) { const message = error instanceof Error ? error.message : String(error); return { content: [ this.textContent(`Error in PMC ID Converter: ${message}`), ], isError: true, }; } }, ); } } export class PMCOpenAccessServiceTool extends BaseTool { register(): void { this.context.server.tool( "pmc_oa_service", "Check if a PMC article is available in the Open Access subset and get download links for full-text content. Works with PMC IDs, PubMed IDs, or DOIs.", { id: z.string().describe("PMC ID, PMID, or DOI"), format: z .enum(["xml", "json"]) .optional() .default("xml") .describe("Output format"), }, async ({ id, format }) => { try { if (!id || id.trim() === "") { throw new Error("ID cannot be empty"); } // Build the PMC OA service URL - this service only works for articles in PMC Open Access Subset const url = `https://www.ncbi.nlm.nih.gov/pmc/utils/oa/oa.fcgi?id=${encodeURIComponent(id.trim())}&tool=entrez-mcp-server&email=entrez-mcp-server%40example.com`; const response = await fetch(url, { headers: { "User-Agent": "NCBI Entrez E-utilities MCP Server (entrez-mcp-server@example.com)", }, }); const data = await response.text(); if (!response.ok) { return { content: [ this.textContent( `PMC Open Access Service request failed: ${response.status} ${response.statusText}`, ), ], isError: true, }; } if ( data.includes("cannotDisseminateFormat") || data.includes("not available") ) { return { content: [ this.textContent( `PMC Open Access Service Results: Article ${id} is not available in the Open Access subset.`, ), ], isError: true, }; } return { content: [ { type: "text", text: `PMC Open Access Service Results:\n\n${this.formatResponseData(data)}`, }, ], }; } catch (error) { const message = error instanceof Error ? error.message : String(error); return { content: [ this.textContent(`Error in PMC Open Access Service: ${message}`), ], isError: true, }; } }, ); } } export class PMCCitationExporterTool extends BaseTool { register(): void { this.context.server.tool( "pmc_citation_exporter", "Export properly formatted citations for PMC articles in various bibliographic formats including RIS, NBIB, MEDLINE, and BibTeX for use in reference managers.", { id: z.string().describe("PMC ID or PMID"), format: z .enum(["ris", "nbib", "medline", "bibtex"]) .describe("Citation format"), }, async ({ id, format }) => { try { if (!id || id.trim() === "") { throw new Error("ID cannot be empty"); } // Build the PMC citation exporter URL based on documentation examples // Format: https://api.ncbi.nlm.nih.gov/lit/ctxp/v1/pmc/{format}?id={id} const url = `https://api.ncbi.nlm.nih.gov/lit/ctxp/v1/pmc/${format}?id=${encodeURIComponent(id.trim())}`; const response = await fetch(url, { headers: { "User-Agent": `${this.context.defaultTool} (${this.context.defaultEmail})`, }, }); const data = await response.text(); if (!response.ok) { return { content: [ this.textContent( `PMC Citation Exporter request failed: ${response.status} ${response.statusText}`, ), ], isError: true, }; } return { content: [ { type: "text", text: `PMC Citation Exporter Results:\n\n${this.formatResponseData(data)}`, }, ], }; } catch (error) { const message = error instanceof Error ? error.message : String(error); return { content: [ this.textContent( `Error in PMC Citation Exporter: ${message}`, ), ], isError: true, }; } }, ); } }