mcp-pubmed

Instructions

Implementation Reference

• src/tools.ts:173-221 (handler)

  The getFullTextLinks handler function that retrieves full text links for a PubMed article by calling NCBI's elink API. It fetches both PMC (PubMed Central) links and provider links, returning a JSON response with the PMID, full_text_links array, and a boolean indicating if free full text is available.

  export async function getFullTextLinks(args: z.infer<typeof getFullTextLinksSchema>): Promise<string> {
    // Use elink to find PMC links and provider links
    const result = await client.elinkCmd([args.pmid], "llinks", "pubmed") as {
      linksets?: Array<{
        idurllist?: Array<{
          objurls?: Array<{
            url?: { value?: string };
            linkname?: string;
            provider?: { name?: string[] };
            categories?: Array<{ category?: string }>;
          }>;
        }>;
      }>;
    };
  
    // Also check for PMC link
    const pmcResult = await client.elink([args.pmid], "pubmed_pmc", "pubmed", "pmc") as {
      linksets?: Array<{ linksetdbs?: Array<{ links?: string[] }> }>;
    };
  
    const pmcIds = pmcResult.linksets?.[0]?.linksetdbs?.[0]?.links || [];
    const links: Array<Record<string, string>> = [];
  
    if (pmcIds.length > 0) {
      links.push({
        source: "PubMed Central",
        url: `https://www.ncbi.nlm.nih.gov/pmc/articles/PMC${pmcIds[0]}/`,
        pmcid: `PMC${pmcIds[0]}`,
      });
    }
  
    // Extract provider links
    const urlList = result.linksets?.[0]?.idurllist?.[0]?.objurls || [];
    for (const obj of urlList) {
      const url = obj.url?.value;
      if (url) {
        links.push({
          source: obj.provider?.name?.[0] || obj.linkname || "Unknown",
          url,
        });
      }
    }
  
    return JSON.stringify({
      pmid: args.pmid,
      full_text_links: links,
      has_free_full_text: links.length > 0,
    }, null, 2);
  }

• src/tools.ts:35-37 (schema)

  The Zod schema definition for getFullTextLinks that validates the input parameters. It requires a single parameter: pmid (PubMed ID as a string).

  export const getFullTextLinksSchema = z.object({
    pmid: z.string().describe("PubMed ID to find full text links for"),
  });

• src/index.ts:70-77 (registration)

  Tool registration that registers get_full_text_links with the MCP server. It includes the tool name, description, schema shape, and the handler that calls getFullTextLinks with parsed arguments.

  server.tool(
    "get_full_text_links",
    "Get links to free full text versions of an article (e.g., PubMed Central). Returns PMC links and publisher free-access URLs.",
    getFullTextLinksSchema.shape,
    async (args) => ({
      content: [{ type: "text", text: await getFullTextLinks(getFullTextLinksSchema.parse(args)) }],
    })
  );