mcp-pubmed

Instructions

Implementation Reference

• src/tools.ts:132-171 (handler)

  The main handler function searchMesh that implements the search_mesh tool logic. It searches the MeSH database using esearch.fcgi, fetches summaries with esummary.fcgi, and returns formatted results including term names, scope notes, and tree numbers.

  export async function searchMesh(args: z.infer<typeof searchMeshSchema>): Promise<string> {
    const searchResult = await client.fetchJson("esearch.fcgi", {
      db: "mesh",
      term: args.query,
      retmax: String(args.max_results),
    }) as { esearchresult: { idlist: string[]; count: string } };
  
    const ids = searchResult.esearchresult.idlist;
    if (ids.length === 0) {
      return JSON.stringify({ total_count: 0, terms: [] }, null, 2);
    }
  
    // Fetch MeSH summaries
    const summaryResult = await client.fetchJson("esummary.fcgi", {
      db: "mesh",
      id: ids.join(","),
      version: "2.0",
    }) as { result?: Record<string, unknown> };
  
    const terms: Array<Record<string, unknown>> = [];
    if (summaryResult.result) {
      for (const id of ids) {
        const entry = summaryResult.result[id] as Record<string, unknown> | undefined;
        if (entry) {
          terms.push({
            uid: id,
            name: entry.ds_meshterms || entry.ds_meshui || id,
            scope_note: entry.ds_scopenote || "",
            tree_numbers: entry.ds_treenumberlist || [],
          });
        }
      }
    }
  
    return JSON.stringify({
      total_count: parseInt(searchResult.esearchresult.count),
      showing: terms.length,
      terms,
    }, null, 2);
  }

• src/tools.ts:30-33 (schema)

  The searchMeshSchema Zod schema defining the input validation for search_mesh tool, with query (string) and max_results (number 1-50, default 10) parameters.

  export const searchMeshSchema = z.object({
    query: z.string().describe("MeSH term search query"),
    max_results: z.number().min(1).max(50).default(10).describe("Maximum results"),
  });

• src/index.ts:61-68 (registration)

  Tool registration where search_mesh is registered with the MCP server, including its description and the handler binding to searchMesh function.

  server.tool(
    "search_mesh",
    "Search the Medical Subject Headings (MeSH) vocabulary. Useful for finding standardized biomedical terms, tree numbers, and scope notes.",
    searchMeshSchema.shape,
    async (args) => ({
      content: [{ type: "text", text: await searchMesh(searchMeshSchema.parse(args)) }],
    })
  );