WormBase MCP Server

Instructions

Implementation Reference

• src/index.ts:64-84 (registration)

  MCP server.tool registration for 'get_protein', including tool description, Zod input schema for protein ID and optional widgets, and inline async handler that fetches data via WormBaseClient and returns JSON-formatted response or error.

  server.tool(
    "get_protein",
    "Get detailed information about a protein including sequence, domains, motifs, and structure.",
    {
      id: z.string().describe("Protein identifier - WormBase protein ID"),
      widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, sequences, motif_details, external_links, references"),
    },
    async ({ id, widgets }) => {
      try {
        const data = await client.getEntity("protein", id, widgets);
        return {
          content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
        };
      } catch (error) {
        return {
          content: [{ type: "text", text: `Error fetching protein: ${error}` }],
          isError: true,
        };
      }
    }
  );

• src/index.ts:71-83 (handler)

  Inline handler function executing the core logic of the get_protein tool: retrieves protein entity data using client.getEntity with type 'protein', stringifies to JSON, handles errors.

  async ({ id, widgets }) => {
    try {
      const data = await client.getEntity("protein", id, widgets);
      return {
        content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
      };
    } catch (error) {
      return {
        content: [{ type: "text", text: `Error fetching protein: ${error}` }],
        isError: true,
      };
    }
  }

• src/index.ts:67-70 (schema)

  Zod schema for get_protein tool inputs: required 'id' string (WormBase protein ID), optional 'widgets' array specifying data sections like sequences, motifs.

  {
    id: z.string().describe("Protein identifier - WormBase protein ID"),
    widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, sequences, motif_details, external_links, references"),
  },

• src/client.ts:111-132 (helper)

  WormBaseClient.getEntity helper method called by get_protein handler; fetches specified widgets from WormBase REST API for any entity type (hardcoded 'protein' in handler), cleans 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;
  }

• src/types.ts:69-75 (schema)

  TypeScript const array defining available widgets specifically for protein entities, referenced in the tool's schema description.

  export const PROTEIN_WIDGETS = [
    ...COMMON_WIDGETS,
    "sequences",
    "motif_details",
    "homology",
    "blast_details",
  ] as const;