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);