PubMed Search

Instructions

Implementation Reference

• src/index.ts:142-174 (handler)

  Inline asynchronous handler function for the 'search_pubmed' tool. Processes input parameters, handles date range logic, invokes searchHandler.search, and formats the response as MCP content.

  async ({ query, searchOptions }) => {
    try {
      const options = { ...(searchOptions || {}) };
  
      // If dateFrom is provided but dateTo is missing, set dateTo to today's date
      if (options.dateFrom && !options.dateTo) {
        const now = new Date();
        const yyyy = now.getFullYear();
        const mm = String(now.getMonth() + 1).padStart(2, '0');
        const dd = String(now.getDate()).padStart(2, '0');
        options.dateTo = `${yyyy}/${mm}/${dd}`;
      }
  
      const results = await searchHandler.search(query, options);
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(results, null, 2),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error searching PubMed: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
      };
    }
  }

• src/index.ts:125-140 (schema)

  Zod input schema definition for the 'search_pubmed' tool, defining 'query' as required string and optional 'searchOptions' object with retMax, retStart, sort, dateFrom, dateTo.

  inputSchema: {
    query: z.string().describe('Search query for PubMed'),
    searchOptions: z
      .object({
        retMax: z.number().optional().describe('Maximum number of results to return'),
        retStart: z.number().optional().describe('Starting index for results'),
        sort: z
          .enum(['relevance', 'pub_date', 'author', 'journal'])
          .optional()
          .describe('Sort order for results'),
        dateFrom: z.string().optional().describe('Start date filter (YYYY/MM/DD format)'),
        dateTo: z.string().optional().describe('End date filter (YYYY/MM/DD format)(If dateFrom is provided but dateTo is missing, set dateTo to today\'s date)'),
      })
      .optional()
      .describe('Optional search parameters'),
  },

• src/index.ts:120-175 (registration)

  Complete registration of the 'search_pubmed' MCP tool using server.registerTool, including metadata, Zod input schema, and the primary handler function.

  server.registerTool(
    'search_pubmed',
    {
      title: 'PubMed Search',
      description: 'Search PubMed for scientific articles.',
      inputSchema: {
        query: z.string().describe('Search query for PubMed'),
        searchOptions: z
          .object({
            retMax: z.number().optional().describe('Maximum number of results to return'),
            retStart: z.number().optional().describe('Starting index for results'),
            sort: z
              .enum(['relevance', 'pub_date', 'author', 'journal'])
              .optional()
              .describe('Sort order for results'),
            dateFrom: z.string().optional().describe('Start date filter (YYYY/MM/DD format)'),
            dateTo: z.string().optional().describe('End date filter (YYYY/MM/DD format)(If dateFrom is provided but dateTo is missing, set dateTo to today\'s date)'),
          })
          .optional()
          .describe('Optional search parameters'),
      },
    },
    async ({ query, searchOptions }) => {
      try {
        const options = { ...(searchOptions || {}) };
  
        // If dateFrom is provided but dateTo is missing, set dateTo to today's date
        if (options.dateFrom && !options.dateTo) {
          const now = new Date();
          const yyyy = now.getFullYear();
          const mm = String(now.getMonth() + 1).padStart(2, '0');
          const dd = String(now.getDate()).padStart(2, '0');
          options.dateTo = `${yyyy}/${mm}/${dd}`;
        }
  
        const results = await searchHandler.search(query, options);
        return {
          content: [
            {
              type: 'text',
              text: JSON.stringify(results, null, 2),
            },
          ],
        };
      } catch (error) {
        return {
          content: [
            {
              type: 'text',
              text: `Error searching PubMed: ${error instanceof Error ? error.message : 'Unknown error'}`,
            },
          ],
        };
      }
    }
  );

• src/handlers/search.ts:13-27 (helper)

  Factory function createSearchHandler that initializes PubMed API client and returns a search handler object. The search method calls pubmedApi.searchAndFetch and maps results to {pmid, title, pubDate}.

  export function createSearchHandler(pubmedOptions: PubMedOptions): SearchHandler {
    const pubmedApi = createPubMedAPI(pubmedOptions);
  
    return {
      async search(query: string, searchOptions?: SearchOptions): Promise<SearchResultItem[]> {
        const articles = await pubmedApi.searchAndFetch(query, searchOptions);
        
        return articles.map(article => ({
          pmid: article.pmid,
          title: article.title,
          pubDate: article.pubDate
        }));
      }
    };
  }

• src/pubmed-api.ts:568-572 (helper)

  Core searchAndFetch method in PubMedAPI implementation. Performs ESearch for PMIDs then fetches article details via EFetch, implementing the actual PubMed API interaction for search_pubmed tool.

  const searchAndFetch = async (query: string, options: SearchAndFetchOptions = {}): Promise<Article[]> => {
    const { maxResults = 20, ...searchOptions } = options;
    const searchResult = await search(query, { ...searchOptions, retMax: maxResults });
    return fetchArticles(searchResult.idList);
  };