ProteinAtlas MCP Server

Instructions

Implementation Reference

• src/index.ts:837-863 (handler)

  Main handler function for 'get_protein_info' tool that validates input, fetches protein data, and returns JSON response or error.

  private async handleGetProteinInfo(args: any) {
    if (!isValidGeneArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid gene arguments');
    }
  
    try {
      const result = await this.fetchProteinData(args.gene, args.format || 'json');
      return {
        content: [
          {
            type: 'text',
            text: typeof result === 'object' ? JSON.stringify(result, null, 2) : String(result),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error fetching protein info: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:63-73 (schema)

  Input validation type guard 'isValidGeneArgs' used by the handler to check gene symbol and format parameters.

  const isValidGeneArgs = (
    args: any
  ): args is { gene: string; format?: string } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      typeof args.gene === 'string' &&
      args.gene.length > 0 &&
      (args.format === undefined || ['json', 'tsv', 'xml', 'trig'].includes(args.format))
    );
  };

• src/index.ts:459-470 (registration)

  Tool registration in ListToolsRequestSchema handler, including name, description, and input schema definition.

  {
    name: 'get_protein_info',
    description: 'Get detailed information for a specific protein by gene symbol',
    inputSchema: {
      type: 'object',
      properties: {
        gene: { type: 'string', description: 'Gene symbol (e.g., BRCA1, TP53)' },
        format: { type: 'string', enum: ['json', 'tsv', 'xml', 'trig'], description: 'Output format (default: json)' },
      },
      required: ['gene'],
    },
  },

• src/index.ts:671-672 (registration)

  Dispatch registration in CallToolRequestSchema switch statement routing to the handler.

  case 'get_protein_info':
    return this.handleGetProteinInfo(args);

• src/index.ts:738-741 (helper)

  Core helper method called by handler to fetch protein data via API search.

  private async fetchProteinData(gene: string, format: string = 'json'): Promise<any> {
    // Use searchProteins method which properly handles columns parameter
    return this.searchProteins(gene, format, undefined, 1);
  }