ProteinAtlas MCP Server

Instructions

Implementation Reference

• src/index.ts:1138-1164 (handler)

  The main handler function for the 'get_antibody_info' tool. Validates input using isValidGeneArgs, fetches antibody information using the helper method, formats as JSON text response, or returns error.

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

• src/index.ts:589-600 (registration)

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

  {
    name: 'get_antibody_info',
    description: 'Get antibody validation and staining information 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:773-776 (helper)

  Helper method that performs the API call to retrieve antibody information by searching with specific antibody-related columns.

  private async fetchAntibodyInfo(gene: string): Promise<any> {
    const columns = ['g', 'eg', 'ab', 'abrr', 'relih', 'relmb', 'relce'];
    return this.searchProteins(gene, 'json', columns, 1);
  }

• src/index.ts:695-696 (registration)

  Dispatcher case in CallToolRequestSchema handler that routes calls to the specific tool handler.

  case 'get_antibody_info':
    return this.handleGetAntibodyInfo(args);