ProteinAtlas MCP Server

Instructions

Implementation Reference

• src/index.ts:1071-1097 (handler)

  The main handler function for the 'get_pathology_data' tool. Validates input using isValidGeneArgs, fetches pathology data via fetchPathologyData, and returns the JSON-formatted result or an error response.

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

• src/index.ts:565-572 (schema)

  Input schema for the 'get_pathology_data' tool, defining 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:562-573 (registration)

  Tool registration in the tools list, specifying name, description, and input schema for MCP server.setTools.

  {
    name: 'get_pathology_data',
    description: 'Get cancer and pathology 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:690-691 (registration)

  Dispatcher switch case in the CallToolRequestHandler that routes 'get_pathology_data' calls to the handler method.

  case 'get_pathology_data':
    return this.handleGetPathologyData(args);

• src/index.ts:758-761 (helper)

  Helper method that performs the core data fetch for pathology data by calling searchProteins with specific prognostic columns.

  private async fetchPathologyData(gene: string): Promise<any> {
    const columns = ['g', 'eg', 'prognostic_Breast_Invasive_Carcinoma_(TCGA)', 'prognostic_Colon_Adenocarcinoma_(TCGA)', 'prognostic_Lung_Adenocarcinoma_(TCGA)', 'prognostic_Prostate_Adenocarcinoma_(TCGA)'];
    return this.searchProteins(gene, 'json', columns, 1);
  }