WormBase MCP Server

Instructions

Implementation Reference

• src/index.ts:230-242 (handler)

  MCP tool handler for get_ontology: calls client.getOntology(id), returns JSON stringified data as text content or error response.

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

• src/index.ts:227-229 (schema)

  Input schema for the get_ontology tool: requires a gene identifier string.

  {
    id: z.string().describe("Gene identifier"),
  },

• src/index.ts:224-243 (registration)

  Registration of the get_ontology MCP tool using server.tool, including description, input schema, and handler function.

  server.tool(
    "get_ontology",
    "Get Gene Ontology (GO) terms for a gene including molecular function, biological process, and cellular component annotations.",
    {
      id: z.string().describe("Gene identifier"),
    },
    async ({ id }) => {
      try {
        const data = await client.getOntology(id);
        return {
          content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
        };
      } catch (error) {
        return {
          content: [{ type: "text", text: `Error fetching ontology: ${error}` }],
          isError: true,
        };
      }
    }
  );

• src/client.ts:178-182 (helper)

  Core helper function in WormBaseClient that performs the HTTP request to WormBase REST API for gene ontology data and processes it with cleanWidgetData.

  async getOntology(id: string): Promise<Record<string, unknown>> {
    const url = `${this.baseUrl}/rest/widget/gene/${encodeURIComponent(id)}/ontology`;
    const data = await this.fetch<any>(url);
    return this.cleanWidgetData(data);
  }