mcp-pubmed

Instructions

Implementation Reference

• src/tools.ts:80-102 (handler)

  The getCitations function that executes the tool logic. It queries NCBI's elink API to find articles that cite a given PMID, fetches article details for up to 20 citing articles, and returns a JSON response with the citing count and article summaries.

  export async function getCitations(args: z.infer<typeof getCitationsSchema>): Promise<string> {
    const result = await client.elink([args.pmid], "pubmed_pubmed_citedin") as {
      linksets?: Array<{ linksetdbs?: Array<{ links?: string[] }> }>;
    };
  
    const links = result.linksets?.[0]?.linksetdbs?.[0]?.links || [];
  
    if (links.length === 0) {
      return JSON.stringify({ pmid: args.pmid, citing_count: 0, citing_articles: [] }, null, 2);
    }
  
    // Fetch summaries for citing articles (max 20)
    const fetchIds = links.slice(0, 20);
    const xml = await client.efetch(fetchIds);
    const articles = parseArticles(xml);
  
    return JSON.stringify({
      pmid: args.pmid,
      citing_count: links.length,
      showing: articles.length,
      citing_articles: articles.map(formatArticleSummary),
    }, null, 2);
  }

• src/tools.ts:21-23 (schema)

  The getCitationsSchema defines input validation for the tool, accepting a single 'pmid' string parameter (PubMed ID to find citing articles for).

  export const getCitationsSchema = z.object({
    pmid: z.string().describe("PubMed ID to find citing articles for"),
  });

• src/index.ts:43-50 (registration)

  The get_citations tool is registered with the MCP server, mapping the schema shape to the getCitations handler function with a description explaining its forward citation tracking purpose.

  server.tool(
    "get_citations",
    "Get articles that cite a given PubMed article (PMID). Useful for forward citation tracking.",
    getCitationsSchema.shape,
    async (args) => ({
      content: [{ type: "text", text: await getCitations(getCitationsSchema.parse(args)) }],
    })
  );

• src/tools.ts:223-233 (helper)

  The formatArticleSummary helper function used by getCitations to format article metadata (PMID, title, authors, journal, publication date, DOI, and abstract) into a concise summary object.

  function formatArticleSummary(a: ArticleMetadata) {
    return {
      pmid: a.pmid,
      title: a.title,
      authors: a.authors.slice(0, 5).join(", ") + (a.authors.length > 5 ? " et al." : ""),
      journal: a.journal,
      pub_date: a.pubDate,
      doi: a.doi || undefined,
      abstract: a.abstract.length > 500 ? a.abstract.slice(0, 500) + "..." : a.abstract,
    };
  }