WormBase MCP Server

Instructions

Implementation Reference

• src/index.ts:270-289 (registration)

  Registers the 'get_paper' MCP tool with name, description, input schema (id: string), and an inline async handler that fetches paper data using WormBaseClient.getEntity and returns JSON-formatted response or error.
  server.tool( "get_paper", "Get information about a scientific paper/publication including authors, abstract, and associated genes.", { id: z.string().describe("Paper identifier - WormBase paper ID (e.g., 'WBPaper00000001') or PubMed ID"), }, async ({ id }) => { try { const data = await client.getEntity("paper", id, ["overview", "referenced_genes"]); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching paper: ${error}` }], isError: true, }; } } );
• src/index.ts:276-288 (handler)

  Inline handler function for the get_paper tool. Calls WormBaseClient.getEntity for type 'paper' with widgets ['overview', 'referenced_genes'], serializes to JSON text response.
  async ({ id }) => { try { const data = await client.getEntity("paper", id, ["overview", "referenced_genes"]); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching paper: ${error}` }], isError: true, }; } }
• src/index.ts:273-275 (schema)

  Zod input schema for get_paper tool: requires 'id' string parameter (WormBase paper ID or PubMed ID).
  { id: z.string().describe("Paper identifier - WormBase paper ID (e.g., 'WBPaper00000001') or PubMed ID"), },
• src/client.ts:111-132 (helper)

  WormBaseClient.getEntity generic helper method implementing the core API fetch logic for any WormBase entity (including 'paper'), retrieving specified widgets from REST API and cleaning the data.
  async getEntity( type: EntityType, id: string, widgets?: string[] ): Promise<Record<string, unknown>> { const defaultWidgets = ["overview"]; const requestedWidgets = widgets || defaultWidgets; const result: Record<string, unknown> = { id, type }; for (const widget of requestedWidgets) { try { const url = `${this.baseUrl}/rest/widget/${type}/${encodeURIComponent(id)}/${widget}`; const data = await this.fetch<any>(url); result[widget] = this.cleanWidgetData(data); } catch (error) { result[widget] = { error: `Failed to fetch ${widget}` }; } } return result; }