search_pubmed
Search PubMed to find medical and life science literature using customizable filters for publication type, date range, and sorting options.
Instructions
Search PubMed for medical and life science literature
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| query | Yes | Search query for medical literature (e.g., "COVID-19 treatment", "cancer immunotherapy", "diabetes management") | |
| maxResults | No | Maximum number of articles to return (1-200) | |
| sort | No | Sort order: relevance, date | relevance |
| publicationType | No | Filter by publication type: all, review, clinical_trial, meta_analysis, case_report | all |
| dateRange | No | Date range filter: all, 1year, 5years, 10years | all |
Implementation Reference
- The main handler function that executes the search_pubmed tool. It processes input arguments, calls the PubMedAPIClient's searchPubMed method, handles the API response, and returns formatted results or error information.
execute: async (args: any) => { const { query, maxResults = 20, sort = 'relevance', publicationType = 'all', dateRange = 'all' } = args; try { const startTime = Date.now(); // 使用真正的PubMed API const result = await client.searchPubMed(query, { maxResults, sort, publicationType, dateRange }); const searchTime = Date.now() - startTime; return { success: true, data: { source: 'PubMed API', query, sort, publicationType, dateRange, totalResults: result.count, articles: result.articles, searchTime, timestamp: Date.now(), apiUsed: true, searchMetadata: { database: 'PubMed', searchStrategy: 'E-utilities API', filters: { publicationType: publicationType !== 'all' ? publicationType : null, dateRange: dateRange !== 'all' ? dateRange : null, sort } } } }; } catch (error) { // 如果API失败，提供有用的错误信息 return { success: false, error: `PubMed search failed: ${error instanceof Error ? error.message : String(error)}`, data: { source: 'PubMed', query, articles: [], totalResults: 0, apiUsed: false, suggestions: [ 'Check your internet connection', 'Try simpler search terms', 'Use medical subject headings (MeSH terms)', 'Try again in a few moments' ] } }; } } - Input schema defining the parameters for the search_pubmed tool: query (required), maxResults, sort, publicationType, and dateRange.
inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Search query for medical literature (e.g., "COVID-19 treatment", "cancer immunotherapy", "diabetes management")' }, maxResults: { type: 'number', description: 'Maximum number of articles to return (1-200)', default: 20, minimum: 1, maximum: 200 }, sort: { type: 'string', description: 'Sort order: relevance, date', default: 'relevance', enum: ['relevance', 'date'] }, publicationType: { type: 'string', description: 'Filter by publication type: all, review, clinical_trial, meta_analysis, case_report', default: 'all', enum: ['all', 'review', 'clinical_trial', 'meta_analysis', 'case_report'] }, dateRange: { type: 'string', description: 'Date range filter: all, 1year, 5years, 10years', default: 'all', enum: ['all', '1year', '5years', '10years'] } }, required: ['query'] }, - src/tools/academic/pubmed-tools.ts:159-261 (registration)Registration of the search_pubmed tool in the registerPubMedTools function, specifying name, description, category, source, inputSchema, and execute handler.
registry.registerTool({ name: 'search_pubmed', description: 'Search PubMed for medical and life science literature', category: 'academic', source: 'PubMed', inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Search query for medical literature (e.g., "COVID-19 treatment", "cancer immunotherapy", "diabetes management")' }, maxResults: { type: 'number', description: 'Maximum number of articles to return (1-200)', default: 20, minimum: 1, maximum: 200 }, sort: { type: 'string', description: 'Sort order: relevance, date', default: 'relevance', enum: ['relevance', 'date'] }, publicationType: { type: 'string', description: 'Filter by publication type: all, review, clinical_trial, meta_analysis, case_report', default: 'all', enum: ['all', 'review', 'clinical_trial', 'meta_analysis', 'case_report'] }, dateRange: { type: 'string', description: 'Date range filter: all, 1year, 5years, 10years', default: 'all', enum: ['all', '1year', '5years', '10years'] } }, required: ['query'] }, execute: async (args: any) => { const { query, maxResults = 20, sort = 'relevance', publicationType = 'all', dateRange = 'all' } = args; try { const startTime = Date.now(); // 使用真正的PubMed API const result = await client.searchPubMed(query, { maxResults, sort, publicationType, dateRange }); const searchTime = Date.now() - startTime; return { success: true, data: { source: 'PubMed API', query, sort, publicationType, dateRange, totalResults: result.count, articles: result.articles, searchTime, timestamp: Date.now(), apiUsed: true, searchMetadata: { database: 'PubMed', searchStrategy: 'E-utilities API', filters: { publicationType: publicationType !== 'all' ? publicationType : null, dateRange: dateRange !== 'all' ? dateRange : null, sort } } } }; } catch (error) { // 如果API失败，提供有用的错误信息 return { success: false, error: `PubMed search failed: ${error instanceof Error ? error.message : String(error)}`, data: { source: 'PubMed', query, articles: [], totalResults: 0, apiUsed: false, suggestions: [ 'Check your internet connection', 'Try simpler search terms', 'Use medical subject headings (MeSH terms)', 'Try again in a few moments' ] } }; } } }); - Core helper method in PubMedAPIClient that handles PubMed ESearch and ESummary API calls to retrieve article search results.
async searchPubMed(query: string, options: any = {}) { // 第一步：搜索获取PMID列表 const searchParams = { db: 'pubmed', term: query, retmax: options.maxResults || 20, sort: options.sort === 'date' ? 'pub_date' : 'relevance', datetype: 'pdat' }; // 添加日期过滤 if (options.dateRange && options.dateRange !== 'all') { const now = new Date(); let startDate; switch (options.dateRange) { case '1year': startDate = new Date(now.getFullYear() - 1, now.getMonth(), now.getDate()); break; case '5years': startDate = new Date(now.getFullYear() - 5, now.getMonth(), now.getDate()); break; case '10years': startDate = new Date(now.getFullYear() - 10, now.getMonth(), now.getDate()); break; } if (startDate) { const startDateStr = startDate.toISOString().split('T')[0].replace(/-/g, '/'); const endDateStr = now.toISOString().split('T')[0].replace(/-/g, '/'); searchParams.term += ` AND ("${startDateStr}"[Date - Publication] : "${endDateStr}"[Date - Publication])`; } } // 添加出版物类型过滤 if (options.publicationType && options.publicationType !== 'all') { const typeMap: Record<string, string> = { 'review': 'Review[Publication Type]', 'clinical_trial': 'Clinical Trial[Publication Type]', 'meta_analysis': 'Meta-Analysis[Publication Type]', 'case_report': 'Case Reports[Publication Type]' }; const pubType = options.publicationType as string; if (typeMap[pubType]) { searchParams.term += ` AND ${typeMap[pubType]}`; } } const searchResult = await this.makeRequest('esearch.fcgi', searchParams); if (!searchResult.esearchresult || !searchResult.esearchresult.idlist || searchResult.esearchresult.idlist.length === 0) { return { articles: [], count: 0 }; } const pmids = searchResult.esearchresult.idlist; // 第二步：获取详细信息 const summaryParams = { db: 'pubmed', id: pmids.join(','), retmode: 'json' }; const summaryResult = await this.makeRequest('esummary.fcgi', summaryParams); return { articles: this.parseSummaryResult(summaryResult), count: parseInt(searchResult.esearchresult.count) || 0 }; } - src/index.ts:230-230 (registration)Top-level registration call in the main server initialization that invokes registerPubMedTools to add search_pubmed to the tool registry.
registerPubMedTools(this.toolRegistry); // 1 tool: search_pubmed