search_ontologies
Search for biological ontologies by name, description, or domain to find structured vocabularies for biomedical data annotation and integration.
Instructions
Search for ontologies by name, description, or domain
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| query | No | Search query for ontologies (optional for listing all) | |
| also_search_views | No | Include ontology views (default: false) | |
| include_views | No | Include views in results (default: false) | |
| display_context | No | Include JSON-LD context (default: true) | |
| display_links | No | Include hypermedia links (default: true) |
Implementation Reference
- src/index.ts:828-866 (handler)The handler function that implements the core logic of the 'search_ontologies' tool. Validates arguments using isValidSearchOntologiesArgs, constructs API parameters, calls the BioOntology /ontologies endpoint, and returns the JSON response or error.
private async handleSearchOntologies(args: any) { if (!isValidSearchOntologiesArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid search ontologies arguments'); } try { const params: any = { apikey: this.apiKey, }; // Add optional parameters if (args.query) params.q = args.query; if (args.also_search_views !== undefined) params.also_search_views = args.also_search_views; if (args.include_views !== undefined) params.include_views = args.include_views; if (args.display_context !== undefined) params.display_context = args.display_context; if (args.display_links !== undefined) params.display_links = args.display_links; const response = await this.apiClient.get('/ontologies', { params }); return { content: [ { type: 'text', text: JSON.stringify(response.data, null, 2), }, ], }; } catch (error: any) { return { content: [ { type: 'text', text: `Error searching ontologies: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; } } - src/index.ts:570-584 (registration)Tool registration in the ListTools response, defining name, description, and inputSchema for 'search_ontologies'.
{ name: 'search_ontologies', description: 'Search for ontologies by name, description, or domain', inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Search query for ontologies (optional for listing all)' }, also_search_views: { type: 'boolean', description: 'Include ontology views (default: false)' }, include_views: { type: 'boolean', description: 'Include views in results (default: false)' }, display_context: { type: 'boolean', description: 'Include JSON-LD context (default: true)' }, display_links: { type: 'boolean', description: 'Include hypermedia links (default: true)' }, }, required: [], }, }, - src/index.ts:218-236 (schema)Input validation schema (type guard) for search_ontologies arguments, used in the handler to ensure correct parameter types.
const isValidSearchOntologiesArgs = ( args: any ): args is { query?: string; also_search_views?: boolean; include_views?: boolean; display_context?: boolean; display_links?: boolean; } => { return ( typeof args === 'object' && args !== null && (args.query === undefined || typeof args.query === 'string') && (args.also_search_views === undefined || typeof args.also_search_views === 'boolean') && (args.include_views === undefined || typeof args.include_views === 'boolean') && (args.display_context === undefined || typeof args.display_context === 'boolean') && (args.display_links === undefined || typeof args.display_links === 'boolean') ); }; - src/index.ts:705-706 (registration)Dispatch registration in the CallToolRequestSchema switch statement, routing calls to the handleSearchOntologies method.
case 'search_ontologies': return this.handleSearchOntologies(args);