WormBase MCP Server

Instructions

Implementation Reference

• src/client.ts:77-106 (handler)

  Core handler function that implements the get_gene tool logic: resolves non-WBGene IDs using WormMine, fetches data for specified or default widgets from WormBase REST API, cleans the response data, and handles per-widget errors.

  async getGene(
    id: string,
    widgets?: string[]
  ): Promise<Record<string, unknown>> {
    // Resolve gene name to WBGene ID if needed
    let geneId = id;
    if (!id.startsWith("WBGene")) {
      const resolved = await this.resolveGeneId(id);
      if (resolved) {
        geneId = resolved;
      }
    }
  
    const defaultWidgets = ["overview", "phenotype", "expression", "ontology"];
    const requestedWidgets = widgets || defaultWidgets;
  
    const result: Record<string, unknown> = { id: geneId, query: id };
  
    for (const widget of requestedWidgets) {
      try {
        const url = `${this.baseUrl}/rest/widget/gene/${encodeURIComponent(geneId)}/${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/index.ts:41-61 (registration)

  MCP tool registration for 'get_gene', including description, Zod input schema, and thin handler that calls WormBaseClient.getGene and formats response as MCP content.

  server.tool(
    "get_gene",
    "Get detailed information about a C. elegans gene including description, function, expression, phenotypes, and orthologs.",
    {
      id: z.string().describe("Gene identifier - WormBase ID (e.g., 'WBGene00006763') or gene name (e.g., 'daf-2', 'unc-13')"),
      widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, expression, phenotype, interactions, homology, sequences, genetics, external_links, references"),
    },
    async ({ id, widgets }) => {
      try {
        const data = await client.getGene(id, widgets);
        return {
          content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
        };
      } catch (error) {
        return {
          content: [{ type: "text", text: `Error fetching gene: ${error}` }],
          isError: true,
        };
      }
    }
  );

• src/client.ts:60-72 (helper)

  Supporting helper used by getGene to resolve gene names/symbols to canonical WBGene IDs via WormMine search API.

  async resolveGeneId(name: string): Promise<string | null> {
    const url = `${this.wormmineUrl}/search?q=${encodeURIComponent(name)}&facet_Category=Gene&size=1`;
  
    try {
      const response = await this.fetch<any>(url);
      if (response.results?.[0]?.fields?.primaryIdentifier) {
        return response.results[0].fields.primaryIdentifier;
      }
    } catch {
      // Fall through
    }
    return null;
  }

• src/index.ts:44-47 (schema)

  Zod schema defining input parameters for the get_gene tool: required 'id' string and optional 'widgets' array.

  {
    id: z.string().describe("Gene identifier - WormBase ID (e.g., 'WBGene00006763') or gene name (e.g., 'daf-2', 'unc-13')"),
    widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, expression, phenotype, interactions, homology, sequences, genetics, external_links, references"),
  },