PubMed MCP Server

Instructions

Implementation Reference

• src/tool_handler.py:342-378 (handler)

  The _handle_search_mesh_terms method implements the core logic for the search_mesh_terms tool. It validates the 'term' argument, performs a PubMed search using the formatted MeSH query '"{term}"[MeSH Terms]', processes results into formatted summaries with MeSH highlighting, and returns an MCPResponse.

  async def _handle_search_mesh_terms(self, arguments: Dict[str, Any]) -> MCPResponse:
      """Handle MeSH term search."""
      try:
          term = arguments.get("term", "")
          if not term:
              return MCPResponse(
                  content=[{"type": "text", "text": "MeSH term is required"}], is_error=True
              )
  
          max_results = arguments.get("max_results", 20)
  
          # Search using the MeSH term
          search_result = await self.pubmed_client.search_articles(
              query=f'"{term}"[MeSH Terms]', max_results=max_results, cache=self.cache
          )
  
          content = []
          content.append(
              {
                  "type": "text",
                  "text": f"**Articles with MeSH term: {term}**\n\n"
                  f"Total Results: {search_result.total_results:,}\n"
                  f"Showing: {search_result.returned_results}\n",
              }
          )
  
          for i, article_data in enumerate(search_result.articles, 1):
              article_text = self._format_article_summary(article_data, i, highlight_mesh=term)
              content.append({"type": "text", "text": article_text})
  
          return MCPResponse(content=content)
  
      except Exception as e:
          logger.error(f"Error in search_mesh_terms: {e}")
          return MCPResponse(
              content=[{"type": "text", "text": f"Error: {str(e)}"}], is_error=True
          )

• src/tools.py:187-204 (schema)

  The JSON schema definition for the search_mesh_terms tool in TOOL_DEFINITIONS, defining input parameters 'term' (required string) and optional 'max_results' (integer 1-100, default 20).

  {
      "name": "search_mesh_terms",
      "description": ("Search and explore MeSH (Medical Subject Headings) terms"),
      "inputSchema": {
          "type": "object",
          "properties": {
              "term": {"type": "string", "description": "MeSH term to search for"},
              "max_results": {
                  "type": "integer",
                  "minimum": 1,
                  "maximum": 100,
                  "default": 20,
                  "description": "Maximum number of results",
              },
          },
          "required": ["term"],
      },
  },

• src/tool_handler.py:65-78 (registration)

  The handler_map in ToolHandler.handle_tool_call registers the 'search_mesh_terms' tool name to the _handle_search_mesh_terms handler method.

  handler_map = {
      "search_pubmed": self._handle_search_pubmed,
      "get_article_details": self._handle_get_article_details,
      "search_by_author": self._handle_search_by_author,
      "find_related_articles": self._handle_find_related_articles,
      "export_citations": self._handle_export_citations,
      "search_mesh_terms": self._handle_search_mesh_terms,
      "search_by_journal": self._handle_search_by_journal,
      "get_trending_topics": self._handle_get_trending_topics,
      "analyze_research_trends": self._handle_analyze_research_trends,
      "compare_articles": self._handle_compare_articles,
      "get_journal_metrics": self._handle_get_journal_metrics,
      "advanced_search": self._handle_advanced_search,
  }