STRING-db MCP Server

Instructions

Implementation Reference

• src/index.ts:592-649 (handler)

  The handler function that validates input, calls the STRING API enrichment endpoint, parses the TSV response, groups results by category, and returns formatted JSON output.
  private async handleGetFunctionalEnrichment(args: any) { if (!isValidEnrichmentArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid enrichment arguments'); } try { const species = args.species || '9606'; const params: any = { identifiers: args.protein_ids.join('%0d'), species: species, caller_identity: 'string-mcp-server', }; if (args.background_string_identifiers) { params.background_string_identifiers = args.background_string_identifiers.join('%0d'); } const response = await this.apiClient.get('/tsv/enrichment', { params }); const enrichments = this.parseTsvData<EnrichmentTerm>(response.data); // Group by category const groupedEnrichments: Record<string, EnrichmentTerm[]> = {}; enrichments.forEach(term => { if (!groupedEnrichments[term.category]) { groupedEnrichments[term.category] = []; } groupedEnrichments[term.category].push(term); }); return { content: [ { type: 'text', text: JSON.stringify({ query_proteins: args.protein_ids, species: species, total_terms: enrichments.length, enrichment_categories: Object.keys(groupedEnrichments), enrichments: groupedEnrichments, significant_terms: enrichments.filter(term => term.pvalue_fdr < 0.05).length, }, null, 2), }, ], }; } catch (error) { return { content: [ { type: 'text', text: `Error performing functional enrichment: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; } }
• src/index.ts:337-349 (registration)

  Tool registration in the list of tools returned by ListToolsRequestSchema, including name, description, and input schema.
  { name: 'get_functional_enrichment', description: 'Perform functional enrichment analysis on a set of proteins', inputSchema: { type: 'object', properties: { protein_ids: { type: 'array', items: { type: 'string' }, description: 'List of protein identifiers' }, species: { type: 'string', description: 'Species name or NCBI taxonomy ID (default: 9606 for human)' }, background_string_identifiers: { type: 'array', items: { type: 'string' }, description: 'Background protein set for enrichment (optional)' }, }, required: ['protein_ids'], }, },
• src/index.ts:340-348 (schema)

  JSON schema defining the input parameters for the get_functional_enrichment tool.
  inputSchema: { type: 'object', properties: { protein_ids: { type: 'array', items: { type: 'string' }, description: 'List of protein identifiers' }, species: { type: 'string', description: 'Species name or NCBI taxonomy ID (default: 9606 for human)' }, background_string_identifiers: { type: 'array', items: { type: 'string' }, description: 'Background protein set for enrichment (optional)' }, }, required: ['protein_ids'], },
• src/index.ts:99-113 (helper)

  Type guard function that validates the input arguments for the functional enrichment tool.
  const isValidEnrichmentArgs = ( args: any ): args is { protein_ids: string[]; species?: string; background_string_identifiers?: string[] } => { return ( typeof args === 'object' && args !== null && Array.isArray(args.protein_ids) && args.protein_ids.length > 0 && args.protein_ids.every((id: any) => typeof id === 'string') && (args.species === undefined || typeof args.species === 'string') && (args.background_string_identifiers === undefined || (Array.isArray(args.background_string_identifiers) && args.background_string_identifiers.every((id: any) => typeof id === 'string'))) ); };
• src/index.ts:39-50 (helper)

  TypeScript interface defining the structure of enrichment term data returned from the STRING API.
  interface EnrichmentTerm { category: string; term: string; number_of_genes: number; number_of_genes_in_background: number; ncbiTaxonId: number; inputGenes: string; preferredNames: string; pvalue: number; pvalue_fdr: number; description: string; }