search_proteins
Find proteins by name, gene, or identifier across species using the STRING protein interaction database to support network analysis and functional studies.
Instructions
Search for proteins by name or identifier across species
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| query | Yes | Search query (protein name, gene name, or identifier) | |
| species | No | Species name or NCBI taxonomy ID (optional) | |
| limit | No | Maximum number of results (default: 10) |
Implementation Reference
- src/index.ts:757-808 (handler)The core handler function that implements the search_proteins tool. Validates input, queries the STRING API endpoint '/tsv/get_string_ids', parses the TSV response into ProteinAnnotation objects, and formats the results as JSON.private async handleSearchProteins(args: any) { if (!isValidSearchArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid search arguments'); } try { const species = args.species || ''; const limit = args.limit || 10; const params: any = { identifiers: args.query, limit: limit, }; if (species) { params.species = species; } const response = await this.apiClient.get('/tsv/get_string_ids', { params }); const results = this.parseTsvData<ProteinAnnotation>(response.data); return { content: [ { type: 'text', text: JSON.stringify({ query: args.query, species_filter: species || 'all', total_results: results.length, proteins: results.map(protein => ({ string_id: protein.stringId, preferred_name: protein.preferredName, ncbi_taxon_id: protein.ncbiTaxonId, annotation: protein.annotation, protein_size: protein.protein_size, })) }, null, 2), }, ], }; } catch (error) { return { content: [ { type: 'text', text: `Error searching proteins: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; }
- src/index.ts:375-387 (registration)Registration of the search_proteins tool in the ListToolsRequestHandler response, including name, description, and input schema definition.{ name: 'search_proteins', description: 'Search for proteins by name or identifier across species', inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Search query (protein name, gene name, or identifier)' }, species: { type: 'string', description: 'Species name or NCBI taxonomy ID (optional)' }, limit: { type: 'number', description: 'Maximum number of results (default: 10)', minimum: 1, maximum: 100 }, }, required: ['query'], }, },
- src/index.ts:405-406 (registration)Dispatch to the search_proteins handler in the CallToolRequestSchema switch statement.case 'search_proteins': return this.handleSearchProteins(args);
- src/index.ts:130-141 (schema)Type guard function for validating search_proteins input arguments, matching the declared input schema.const isValidSearchArgs = ( args: any ): args is { query: string; species?: string; limit?: number } => { return ( typeof args === 'object' && args !== null && typeof args.query === 'string' && args.query.length > 0 && (args.species === undefined || typeof args.species === 'string') && (args.limit === undefined || (typeof args.limit === 'number' && args.limit > 0 && args.limit <= 100)) ); };
- src/index.ts:417-444 (helper)Utility function used by the handler to parse TSV data from the STRING API into typed objects.private parseTsvData<T>(tsvData: string): T[] { const lines = tsvData.trim().split('\n'); if (lines.length < 2) return []; const headers = lines[0].split('\t'); const results: T[] = []; for (let i = 1; i < lines.length; i++) { const values = lines[i].split('\t'); const obj: any = {}; headers.forEach((header, index) => { const value = values[index] || ''; // Convert numeric fields if (['score', 'nscore', 'fscore', 'pscore', 'ascore', 'escore', 'dscore', 'tscore', 'ncbiTaxonId', 'protein_size', 'number_of_genes', 'number_of_genes_in_background', 'pvalue', 'pvalue_fdr'].includes(header)) { obj[header] = parseFloat(value) || 0; } else { obj[header] = value; } }); results.push(obj as T); } return results; }