ProteinAtlas MCP Server

Instructions

Implementation Reference

• src/index.ts:1166-1217 (handler)

  The main handler function for the 'advanced_search' tool. Validates input, constructs a complex search query using multiple filters (tissue, location, prognostic, etc.), and delegates to the shared searchProteins method.
  private async handleAdvancedSearch(args: any) { if (!isValidAdvancedSearchArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid advanced search arguments'); } try { let searchQuery = args.query || ''; if (args.tissueSpecific) { searchQuery += (searchQuery ? ' AND ' : '') + `tissue:"${args.tissueSpecific}"`; } if (args.subcellularLocation) { searchQuery += (searchQuery ? ' AND ' : '') + `location:"${args.subcellularLocation}"`; } if (args.cancerPrognostic) { searchQuery += (searchQuery ? ' AND ' : '') + `prognostic:"${args.cancerPrognostic}"`; } if (args.proteinClass) { searchQuery += (searchQuery ? ' AND ' : '') + `class:"${args.proteinClass}"`; } if (args.chromosome) { searchQuery += (searchQuery ? ' AND ' : '') + `chromosome:"${args.chromosome}"`; } if (args.antibodyReliability) { searchQuery += (searchQuery ? ' AND ' : '') + `reliability:"${args.antibodyReliability}"`; } if (!searchQuery) { searchQuery = '*'; // Search for everything if no criteria specified } const result = await this.searchProteins(searchQuery, args.format || 'json', args.columns, args.maxResults); return { content: [ { type: 'text', text: typeof result === 'object' ? JSON.stringify(result, null, 2) : String(result), }, ], }; } catch (error) { return { content: [ { type: 'text', text: `Error in advanced search: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; } }
• src/index.ts:87-115 (schema)

  Type guard function for validating advanced_search input arguments.
  const isValidAdvancedSearchArgs = ( args: any ): args is { query?: string; tissueSpecific?: string; subcellularLocation?: string; cancerPrognostic?: string; proteinClass?: string; chromosome?: string; antibodyReliability?: string; format?: string; columns?: string[]; maxResults?: number; } => { return ( typeof args === 'object' && args !== null && (args.query === undefined || typeof args.query === 'string') && (args.tissueSpecific === undefined || typeof args.tissueSpecific === 'string') && (args.subcellularLocation === undefined || typeof args.subcellularLocation === 'string') && (args.cancerPrognostic === undefined || typeof args.cancerPrognostic === 'string') && (args.proteinClass === undefined || typeof args.proteinClass === 'string') && (args.chromosome === undefined || typeof args.chromosome === 'string') && (args.antibodyReliability === undefined || ['approved', 'enhanced', 'supported', 'uncertain'].includes(args.antibodyReliability)) && (args.format === undefined || ['json', 'tsv'].includes(args.format)) && (args.columns === undefined || Array.isArray(args.columns)) && (args.maxResults === undefined || (typeof args.maxResults === 'number' && args.maxResults > 0 && args.maxResults <= 10000)) ); };
• src/index.ts:605-620 (schema)

  JSON Schema definition for the 'advanced_search' tool input, provided in the tool list response.
  inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Base search query' }, tissueSpecific: { type: 'string', description: 'Tissue-specific expression filter' }, subcellularLocation: { type: 'string', description: 'Subcellular localization filter' }, cancerPrognostic: { type: 'string', description: 'Cancer prognostic filter' }, proteinClass: { type: 'string', description: 'Protein class filter' }, chromosome: { type: 'string', description: 'Chromosome filter' }, antibodyReliability: { type: 'string', enum: ['approved', 'enhanced', 'supported', 'uncertain'], description: 'Antibody reliability filter' }, format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' }, columns: { type: 'array', items: { type: 'string' }, description: 'Specific columns to include in results' }, maxResults: { type: 'number', description: 'Maximum number of results (1-10000, default: 100)', minimum: 1, maximum: 10000 }, }, required: [], },
• src/index.ts:602-621 (registration)

  Registration of the 'advanced_search' tool in the list of available tools returned by ListToolsRequestSchema.
  { name: 'advanced_search', description: 'Perform advanced search with multiple filters and criteria', inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Base search query' }, tissueSpecific: { type: 'string', description: 'Tissue-specific expression filter' }, subcellularLocation: { type: 'string', description: 'Subcellular localization filter' }, cancerPrognostic: { type: 'string', description: 'Cancer prognostic filter' }, proteinClass: { type: 'string', description: 'Protein class filter' }, chromosome: { type: 'string', description: 'Chromosome filter' }, antibodyReliability: { type: 'string', enum: ['approved', 'enhanced', 'supported', 'uncertain'], description: 'Antibody reliability filter' }, format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' }, columns: { type: 'array', items: { type: 'string' }, description: 'Specific columns to include in results' }, maxResults: { type: 'number', description: 'Maximum number of results (1-10000, default: 100)', minimum: 1, maximum: 10000 }, }, required: [], }, },
• src/index.ts:698-699 (registration)

  Dispatcher case in the CallToolRequestSchema handler that routes 'advanced_search' calls to the handler function.
  case 'advanced_search': return this.handleAdvancedSearch(args);