search_by_taxonomy
Find UniProt entries by taxonomic classification using NCBI taxonomy IDs or names to retrieve relevant protein data.
Instructions
Search by detailed taxonomic classification
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| taxonomyId | No | NCBI taxonomy ID | |
| taxonomyName | No | Taxonomic name (e.g., Mammalia, Bacteria) | |
| size | No | Number of results to return (1-500, default: 25) |
Implementation Reference
- src/index.ts:1651-1693 (handler)The handler function that executes the tool's logic: validates input using isValidTaxonomySearchArgs, constructs a UniProt search query based on taxonomyId or taxonomyName, fetches results from the UniProt REST API, and returns formatted JSON or error.
private async handleSearchByTaxonomy(args: any) { if (!isValidTaxonomySearchArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid taxonomy search arguments'); } try { let query = 'reviewed:true'; if (args.taxonomyId) { query += ` AND taxonomy_id:"${args.taxonomyId}"`; } if (args.taxonomyName) { query += ` AND taxonomy_name:"${args.taxonomyName}"`; } const response = await this.apiClient.get('/uniprotkb/search', { params: { query: query, format: 'json', size: args.size || 25, }, }); return { content: [ { type: 'text', text: JSON.stringify(response.data, null, 2), }, ], }; } catch (error) { return { content: [ { type: 'text', text: `Error searching by taxonomy: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; } - src/index.ts:639-650 (schema)The input schema definition for the search_by_taxonomy tool, specifying properties for taxonomyId, taxonomyName, and size.
name: 'search_by_taxonomy', description: 'Search by detailed taxonomic classification', inputSchema: { type: 'object', properties: { taxonomyId: { type: 'number', description: 'NCBI taxonomy ID', minimum: 1 }, taxonomyName: { type: 'string', description: 'Taxonomic name (e.g., Mammalia, Bacteria)' }, size: { type: 'number', description: 'Number of results to return (1-500, default: 25)', minimum: 1, maximum: 500 }, }, required: [], }, }, - src/index.ts:770-771 (registration)Registration of the tool handler in the CallToolRequestSchema switch statement, mapping 'search_by_taxonomy' to handleSearchByTaxonomy.
case 'search_by_taxonomy': return this.handleSearchByTaxonomy(args); - src/index.ts:197-208 (helper)Helper validation function (type guard) that checks input arguments conform to the expected schema for search_by_taxonomy.
const isValidTaxonomySearchArgs = ( args: any ): args is { taxonomyId?: number; taxonomyName?: string; size?: number } => { return ( typeof args === 'object' && args !== null && (args.taxonomyId === undefined || (typeof args.taxonomyId === 'number' && args.taxonomyId > 0)) && (args.taxonomyName === undefined || typeof args.taxonomyName === 'string') && (args.size === undefined || (typeof args.size === 'number' && args.size > 0 && args.size <= 500)) && (args.taxonomyId !== undefined || args.taxonomyName !== undefined) ); };