WormBase MCP Server

Instructions

Implementation Reference

• src/index.ts:87-107 (registration)

  MCP tool registration for 'get_phenotype', including description, Zod input schema, and handler function that delegates to WormBaseClient.getEntity

  server.tool(
    "get_phenotype",
    "Get detailed information about a phenotype including associated genes, RNAi experiments, and variations.",
    {
      id: z.string().describe("Phenotype identifier - WormBase phenotype ID (e.g., 'WBPhenotype:0000643')"),
      widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, rnai, variation, transgene, references"),
    },
    async ({ id, widgets }) => {
      try {
        const data = await client.getEntity("phenotype", id, widgets);
        return {
          content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
        };
      } catch (error) {
        return {
          content: [{ type: "text", text: `Error fetching phenotype: ${error}` }],
          isError: true,
        };
      }
    }
  );

• src/index.ts:90-93 (schema)

  Input schema for get_phenotype tool using Zod validation for 'id' and optional 'widgets' array

  {
    id: z.string().describe("Phenotype identifier - WormBase phenotype ID (e.g., 'WBPhenotype:0000643')"),
    widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, rnai, variation, transgene, references"),
  },

• src/index.ts:94-106 (handler)

  Handler function that executes the tool logic: fetches phenotype data via client and returns JSON or error

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

• src/client.ts:111-132 (helper)

  Core helper method getEntity used by the handler to query WormBase REST API for phenotype widgets and clean 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;
  }

• src/client.ts:15-32 (helper)

  Private fetch helper used by getEntity to make HTTP requests to WormBase API

  private async fetch<T>(url: string): Promise<T> {
    const response = await fetch(url, {
      headers: {
        "Accept": "application/json",
        "Accept-Language": "en-US,en;q=0.9",
        "User-Agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/120.0.0.0 Safari/537.36",
        "Sec-Fetch-Dest": "empty",
        "Sec-Fetch-Mode": "cors",
        "Sec-Fetch-Site": "cross-site",
      },
    });
  
    if (!response.ok) {
      throw new Error(`HTTP ${response.status}: ${response.statusText}`);
    }
  
    return response.json() as Promise<T>;
  }