Healthcare MCP Server

Instructions

Implementation Reference

• server/pubmed-tool.js:66-180 (handler)

  The primary handler function for the 'pubmed_search' tool. It performs input validation, caching, constructs PubMed API requests (esearch and esummary), processes article data, and formats the response.
  async searchLiterature(query, maxResults = 5, dateRange = '', openAccess = false) { // Input validation if (!query) { return this.formatErrorResponse('Search query is required'); } // Validate max_results let validMaxResults; try { validMaxResults = parseInt(maxResults); if (validMaxResults < 1) { validMaxResults = 5; } else if (validMaxResults > 100) { validMaxResults = 100; // Limit to reasonable number } } catch (error) { validMaxResults = 5; } // Create cache key const cacheKey = this.getCacheKey('pubmed_search', query, validMaxResults, dateRange, openAccess); // Check cache first const cachedResult = this.cache.get(cacheKey); if (cachedResult) { console.error(`Cache hit for PubMed search: ${query}`); return cachedResult; } try { console.error(`Searching PubMed for: ${query}, max_results=${validMaxResults}, date_range=${dateRange}`); // Process query with date range if provided let processedQuery = query; if (openAccess) { processedQuery += ' AND open access[filter]'; } if (dateRange) { try { const yearsBack = parseInt(dateRange); const currentYear = new Date().getFullYear(); const minYear = currentYear - yearsBack; processedQuery += ` AND ${minYear}:${currentYear}[pdat]`; console.error(`Added date range filter: ${minYear}-${currentYear}`); } catch (error) { // If date_range isn't a valid integer, just ignore it console.error(`Invalid date range: ${dateRange}, ignoring`); } } // Search PubMed to get article IDs const searchParams = { db: 'pubmed', term: processedQuery, retmax: validMaxResults, format: 'json' }; // Add API key if available if (this.apiKey) { searchParams.api_key = this.apiKey; } // Make the search request const searchEndpoint = `${this.baseUrl}esearch.fcgi`; const searchUrl = this.buildUrl(searchEndpoint, searchParams); const searchData = await this.makeRequest(searchUrl); // Extract article IDs and total count const idList = searchData.esearchresult?.idlist || []; const totalResults = parseInt(searchData.esearchresult?.count || 0); // If we have results, fetch article details let articles = []; if (idList.length > 0) { // Prepare parameters for summary request const summaryParams = { db: 'pubmed', id: idList.join(','), retmode: 'json' }; // Add API key if available if (this.apiKey) { summaryParams.api_key = this.apiKey; } // Make the summary request const summaryEndpoint = `${this.baseUrl}esummary.fcgi`; const summaryUrl = this.buildUrl(summaryEndpoint, summaryParams); const summaryData = await this.makeRequest(summaryUrl); // Process article data articles = this.processArticleData(idList, summaryData); } // Create result object const result = this.formatSuccessResponse({ query: query, total_results: totalResults, date_range: dateRange, open_access: openAccess, articles: articles }); // Cache for 12 hours (43200 seconds) this.cache.set(cacheKey, result, 43200); return result; } catch (error) { console.error(`Error searching PubMed: ${error.message}`); return this.formatErrorResponse(`Error searching PubMed: ${error.message}`); } }
• server/index.js:82-108 (schema)

  JSON schema defining the input parameters for the 'pubmed_search' tool, including query (required), max_results, date_range, and open_access.
  inputSchema: { type: "object", properties: { query: { type: "string", description: "Search query for medical literature", }, max_results: { type: "number", description: "Maximum number of results to return", default: 5, minimum: 1, maximum: 100, }, date_range: { type: "string", description: "Limit to articles published within years (e.g. '5' for last 5 years)", default: "", }, open_access: { type: "boolean", description: "Filter for open access articles", default: false, }, }, required: ["query"], },
• server/index.js:80-109 (registration)

  Registration of the 'pubmed_search' tool in the MCP server's list of available tools, including name, description, and input schema.
  name: "pubmed_search", description: "Search for medical literature in PubMed database", inputSchema: { type: "object", properties: { query: { type: "string", description: "Search query for medical literature", }, max_results: { type: "number", description: "Maximum number of results to return", default: 5, minimum: 1, maximum: 100, }, date_range: { type: "string", description: "Limit to articles published within years (e.g. '5' for last 5 years)", default: "", }, open_access: { type: "boolean", description: "Filter for open access articles", default: false, }, }, required: ["query"], }, },
• server/index.js:290-292 (registration)

  Dispatch/registration in the MCP call tool handler switch statement, routing 'pubmed_search' calls to the PubMedTool.searchLiterature method.
  case "pubmed_search": result = await pubmedTool.searchLiterature(args.query, args.max_results, args.date_range, args.open_access); break;
• server/pubmed-tool.js:16-61 (helper)

  Helper method to process raw PubMed summary data into formatted article objects with title, authors, journal, date, URL, and DOI.
  processArticleData(idList, summaryData) { const articles = []; // Get the result data const resultData = summaryData.result || {}; // Process each article for (const articleId of idList) { if (articleId in resultData) { const articleData = resultData[articleId]; // Extract authors const authors = []; if (articleData.authors) { for (const author of articleData.authors) { if (author.name) { authors.push(author.name); } } } // Create article object const article = { id: articleId, title: articleData.title || '', authors: authors, journal: articleData.fulljournalname || '', publication_date: articleData.pubdate || '', abstract_url: `https://pubmed.ncbi.nlm.nih.gov/${articleId}/` }; // Add additional fields if available if (articleData.articleids) { for (const idObj of articleData.articleids) { if (idObj.idtype === 'doi') { article.doi = idObj.value || ''; } } } articles.push(article); } } return articles; }