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[];
  }