WormBase MCP Server

Instructions

Implementation Reference

• src/index.ts:276-288 (handler)

  The handler function for the 'get_paper' tool. It invokes WormBaseClient.getEntity with type 'paper' and specific widgets ['overview', 'referenced_genes'], formats the result as JSON text, and handles errors.

  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 schema defining the input parameters for the 'get_paper' tool: a required string 'id' for the paper identifier.

  {
    id: z.string().describe("Paper identifier - WormBase paper ID (e.g., 'WBPaper00000001') or PubMed ID"),
  },

• src/index.ts:270-289 (registration)

  MCP tool registration for 'get_paper' using McpServer.tool(), specifying name, description, input schema, and handler.

  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/client.ts:111-132 (helper)

  WormBaseClient.getEntity method: generic implementation to fetch data for any WormBase entity type (including 'paper') by querying REST API widgets and cleaning the response.

  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;
  }