mcp-pubmed

Instructions

Implementation Reference

• src/tools.ts:71-78 (handler)

  Main handler function getArticle that executes the tool logic - fetches article XML from NCBI client, parses it using parseArticles utility, and returns the first article as JSON or an error message if not found.

  export async function getArticle(args: z.infer<typeof getArticleSchema>): Promise<string> {
    const xml = await client.efetch([args.pmid]);
    const articles = parseArticles(xml);
    if (articles.length === 0) {
      return JSON.stringify({ error: `No article found for PMID ${args.pmid}` });
    }
    return JSON.stringify(articles[0], null, 2);
  }

• src/tools.ts:17-19 (schema)

  Zod schema definition for getArticleSchema - validates input requiring a pmid (PubMed ID) string parameter.

  export const getArticleSchema = z.object({
    pmid: z.string().describe("PubMed ID"),
  });

• src/index.ts:34-41 (registration)

  MCP server tool registration for 'get_article' - registers the tool with its name, description, schema shape, and async handler that parses arguments and calls getArticle function.

  server.tool(
    "get_article",
    "Get full metadata for a specific PubMed article by PMID, including title, abstract, authors, journal, publication date, DOI, and MeSH terms.",
    getArticleSchema.shape,
    async (args) => ({
      content: [{ type: "text", text: await getArticle(getArticleSchema.parse(args)) }],
    })
  );