Ensembl MCP Server

Instructions

Implementation Reference

• src/index.ts:778-788 (registration)

  Registration of the get_assembly_info tool in the ListToolsRequestSchema response, defining its name, description, and input schema.
  name: 'get_assembly_info', description: 'Get genome assembly information and statistics', inputSchema: { type: 'object', properties: { species: { type: 'string', description: 'Species name (default: homo_sapiens)' }, bands: { type: 'boolean', description: 'Include chromosome banding patterns (default: false)' }, }, required: [], }, },
• src/index.ts:871-872 (registration)

  Maps the tool name to its handler function in the CallToolRequestSchema switch statement.
  case 'get_assembly_info': return this.handleGetAssemblyInfo(args);
• src/index.ts:1524-1551 (handler)

  The handler function that executes the tool: validates args, fetches data from Ensembl REST API endpoint `/info/assembly/{species}`, formats response as JSON, handles errors.
  private async handleGetAssemblyInfo(args: any) { if (!isValidAssemblyArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid assembly info arguments'); } try { const species = this.getDefaultSpecies(args.species); const params: any = {}; if (args.bands) { params.bands = 1; } const response = await this.apiClient.get(`/info/assembly/${species}`, { params }); return { content: [ { type: 'text', text: JSON.stringify(response.data, null, 2), }, ], }; } catch (error) { return this.handleError(error, 'fetching assembly info'); } }
• src/index.ts:272-281 (schema)

  Input validation type guard used in the handler to ensure arguments conform to expected schema.
  const isValidAssemblyArgs = ( args: any ): args is { species?: string; bands?: boolean } => { return ( typeof args === 'object' && args !== null && (args.species === undefined || typeof args.species === 'string') && (args.bands === undefined || typeof args.bands === 'boolean') ); };
• src/index.ts:138-152 (schema)

  TypeScript interface matching the expected response structure from the Ensembl assembly info API.
  interface EnsemblAssemblyInfo { assembly_name: string; assembly_date: string; assembly_accession: string; genebuild_last_geneset_update: string; genebuild_initial_release_date: string; genebuild_start_date: string; genebuild_version: string; genebuild_method: string; golden_path_length: number; total_coding_sequence_length: number; total_genome_length: number; coord_system_versions: string[]; karyotype: string[]; }