Ensembl MCP Server

Instructions

Implementation Reference

• src/index.ts:1481-1498 (handler)

  The handler function for the 'map_coordinates' tool. It fetches coordinate mappings from the Ensembl REST API /map/coords endpoint, converting genomic regions between different assembly versions. Uses helper methods getDefaultSpecies and formatGenomicRegion.

  private async handleMapCoordinates(args: any) {
    try {
      const species = this.getDefaultSpecies(args.species);
      const region = this.formatGenomicRegion(args.region);
  
      const response = await this.apiClient.get(`/map/coords/${species}/${args.target_assembly}/${region}`);
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(response.data, null, 2),
          },
        ],
      };
    } catch (error) {
      return this.handleError(error, 'mapping coordinates');
    }

• src/index.ts:753-764 (registration)

  Tool registration in the ListToolsRequestSchema handler. Defines the name, description, and input schema for the map_coordinates tool.

    name: 'map_coordinates',
    description: 'Convert coordinates between genome assemblies',
    inputSchema: {
      type: 'object',
      properties: {
        region: { type: 'string', description: 'Genomic region (chr:start-end)' },
        species: { type: 'string', description: 'Species name (default: homo_sapiens)' },
        target_assembly: { type: 'string', description: 'Target assembly name' },
      },
      required: ['region', 'target_assembly'],
    },
  },

• src/index.ts:361-373 (schema)

  Type guard function for validating input arguments to the map_coordinates tool, though not called in the handler.

  const isValidMapCoordinatesArgs = (
    args: any
  ): args is { region: string; species?: string; target_assembly: string } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      typeof args.region === 'string' &&
      args.region.length > 0 &&
      (args.species === undefined || typeof args.species === 'string') &&
      typeof args.target_assembly === 'string' &&
      args.target_assembly.length > 0
    );
  };

• src/index.ts:866-867 (registration)

  Dispatch case in the CallToolRequestSchema switch statement that routes calls to the map_coordinates handler.

  case 'map_coordinates':
    return this.handleMapCoordinates(args);