ProteinAtlas MCP Server

Instructions

Implementation Reference

• src/index.ts:1010-1036 (handler)

  The main handler function for the 'get_subcellular_location' tool. Validates input using isValidGeneArgs, fetches data via fetchSubcellularLocalization, and returns JSON-formatted subcellular location data or an error.

  private async handleGetSubcellularLocation(args: any) {
    if (!isValidGeneArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid gene arguments');
    }
  
    try {
      const result = await this.fetchSubcellularLocalization(args.gene);
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(result, null, 2),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error fetching subcellular location: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:538-545 (schema)

  Input schema definition for the tool, specifying required 'gene' parameter and optional format.

  inputSchema: {
    type: 'object',
    properties: {
      gene: { type: 'string', description: 'Gene symbol' },
      format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' },
    },
    required: ['gene'],
  },

• src/index.ts:535-546 (registration)

  Tool registration in the ListToolsRequestSchema handler, defining name, description, and input schema.

  {
    name: 'get_subcellular_location',
    description: 'Get subcellular localization data for a protein',
    inputSchema: {
      type: 'object',
      properties: {
        gene: { type: 'string', description: 'Gene symbol' },
        format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' },
      },
      required: ['gene'],
    },
  },

• src/index.ts:685-686 (registration)

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

  case 'get_subcellular_location':
    return this.handleGetSubcellularLocation(args);

• src/index.ts:753-756 (helper)

  Helper method that fetches subcellular location data by calling searchProteins with specific columns: scl (subcell location), scml (main location), scal (additional locations), relce (reliability).

  private async fetchSubcellularLocalization(gene: string): Promise<any> {
    const columns = ['g', 'eg', 'scl', 'scml', 'scal', 'relce'];
    return this.searchProteins(gene, 'json', columns, 1);
  }