PubMed MCP Server

Instructions

Implementation Reference

• src/tool_handler.py:297-340 (handler)

  Main handler function implementing the export_citations tool: validates PMIDs, fetches article details, formats citations using CitationFormatter, and returns MCPResponse.

  async def _handle_export_citations(self, arguments: Dict[str, Any]) -> MCPResponse:
      """Handle citation export."""
      try:
          pmids = arguments.get("pmids", [])
          if not pmids:
              return MCPResponse(
                  content=[{"type": "text", "text": "PMIDs parameter is required"}], is_error=True
              )
  
          format_type = CitationFormat(arguments.get("format", "bibtex"))
  
          # Get article details
          articles = await self.pubmed_client.get_article_details(
              pmids=pmids,
              include_abstracts=True,  # Always get abstracts for citation
              cache=self.cache,
          )
  
          if not articles:
              return MCPResponse(
                  content=[{"type": "text", "text": "No articles found for the provided PMIDs"}],
                  is_error=True,
              )
  
          # Format citations
          citations = CitationFormatter.format_multiple_citations(
              articles=articles, format_type=format_type
          )
  
          content = []
          content.append(
              {
                  "type": "text",
                  "text": f"**Citations in {format_type.value.upper()} format**\n\n{citations}",
              }
          )
  
          return MCPResponse(content=content)
  
      except Exception as e:
          logger.error(f"Error in export_citations: {e}")
          return MCPResponse(
              content=[{"type": "text", "text": f"Error: {str(e)}"}], is_error=True
          )

• src/tools.py:161-186 (schema)

  JSON schema defining the input parameters for the export_citations tool, including PMIDs (required), format (default bibtex), and include_abstracts.

  {
      "name": "export_citations",
      "description": "Export article citations in various formats",
      "inputSchema": {
          "type": "object",
          "properties": {
              "pmids": {
                  "type": "array",
                  "items": {"type": "string"},
                  "description": "List of PubMed IDs to export",
              },
              "format": {
                  "type": "string",
                  "enum": ["bibtex", "endnote", "ris", "apa", "mla", "chicago", "vancouver"],
                  "default": "bibtex",
                  "description": "Citation format",
              },
              "include_abstracts": {
                  "type": "boolean",
                  "default": False,
                  "description": "Include abstracts in citations",
              },
          },
          "required": ["pmids"],
      },
  },

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

  Tool handler routing map that registers 'export_citations' to its handler function _handle_export_citations.

  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,
  }