PubMed MCP Server

Instructions

Implementation Reference

• src/tool_handler.py:179-218 (handler)

  MCP tool handler _handle_get_article_details: validates input arguments, calls PubMedClient.get_article_details, formats articles using _format_article_details, and constructs MCPResponse.
  async def _handle_get_article_details(self, arguments: Dict[str, Any]) -> MCPResponse: """Handle getting detailed article information.""" try: pmids = arguments.get("pmids", []) if not pmids: return MCPResponse( content=[{"type": "text", "text": "PMIDs parameter is required"}], is_error=True ) include_abstracts = arguments.get("include_abstracts", True) include_citations = arguments.get("include_citations", False) articles = await self.pubmed_client.get_article_details( pmids=pmids, include_abstracts=include_abstracts, include_citations=include_citations, cache=self.cache, ) content = [] content.append( {"type": "text", "text": f"**Article Details for {len(articles)} Articles**\n"} ) if articles: for i, article in enumerate(articles, 1): article_text = self._format_article_details(article, i) content.append({"type": "text", "text": article_text}) else: content.append( {"type": "text", "text": "No articles found for the provided PMIDs."} ) return MCPResponse(content=content) except Exception as e: logger.error(f"Error in get_article_details: {e}") return MCPResponse( content=[{"type": "text", "text": f"Error: {str(e)}"}], is_error=True )
• src/tools.py:95-119 (schema)

  Tool schema definition specifying input parameters: required pmids array, optional include_abstracts and include_citations booleans.
  { "name": "get_article_details", "description": ("Get detailed information for specific articles by PMID"), "inputSchema": { "type": "object", "properties": { "pmids": { "type": "array", "items": {"type": "string"}, "description": "List of PubMed IDs", }, "include_abstracts": { "type": "boolean", "default": True, "description": "Include abstracts in response", }, "include_citations": { "type": "boolean", "default": False, "description": "Include citation count and metrics", }, }, "required": ["pmids"], }, },
• src/tool_handler.py:65-78 (registration)

  Registration of get_article_details tool in the handler_map dictionary, mapping to the _handle_get_article_details 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, }
• src/pubmed_client.py:207-257 (helper)

  PubMedClient.get_article_details: validates PMIDs, checks/sets cache, fetches details via EFetch API using _fetch_article_details and parses into Article objects.
  async def get_article_details( self, pmids: List[str], include_abstracts: bool = True, include_citations: bool = False, cache: Optional[CacheManager] = None, ) -> List[Article]: """ Get detailed article information for specific PMIDs. Args: pmids: List of PubMed IDs include_abstracts: Include abstracts include_citations: Include citation metrics cache: Cache manager instance Returns: List of Article objects """ # Validate PMIDs valid_pmids = [pmid for pmid in pmids if validate_pmid(pmid)] if len(valid_pmids) != len(pmids): logger.warning(f"Some invalid PMIDs provided: {set(pmids) - set(valid_pmids)}") if not valid_pmids: return [] # Check cache if cache: cache_key = cache.generate_key( "article_details", pmids=valid_pmids, include_abstracts=include_abstracts, include_citations=include_citations, ) cached_result = cache.get(cache_key) if cached_result: return [Article(**article) for article in cached_result] articles = await self._fetch_article_details( valid_pmids, include_full_details=True, include_citations=include_citations, ) # Cache the result if cache: cache.set(cache_key, [article.model_dump() for article in articles]) return articles
• src/tool_handler.py:896-947 (helper)

  _format_article_details helper: formats detailed Article object into rich text string for MCP response, including authors, journal, abstract, keywords, MeSH, links.
  def _format_article_details(self, article, index: int) -> str: """Format detailed article information.""" # Authors with affiliations authors_text = "" for i, author in enumerate(article.authors[:5], 1): authors_text += f"{i}. {author.first_name or author.initials or ''} {author.last_name}" if author.affiliation: authors_text += ( f" ({author.affiliation[:50]}...)" if len(author.affiliation) > 50 else f" ({author.affiliation})" ) authors_text += "\n" if len(article.authors) > 5: authors_text += f"... and {len(article.authors) - 5} more authors\n" # Keywords keywords_str = ", ".join(article.keywords[:10]) if article.keywords else "No keywords" # DOI and links links_text = "" if article.doi: links_text += f"DOI: https://doi.org/{article.doi}\n" if article.pmc_id: links_text += f"PMC: https://www.ncbi.nlm.nih.gov/pmc/articles/{article.pmc_id}\n" links_text += f"PubMed: https://pubmed.ncbi.nlm.nih.gov/{article.pmid}\n" article_text = f""" **{index}. {article.title}** **Authors:** {authors_text} **Journal:** {article.journal.title} **Publication Date:** {format_date(article.pub_date)} **Volume/Issue:** {article.journal.volume or 'N/A'}/{article.journal.issue or 'N/A'} **Abstract:** {article.abstract or 'No abstract available'} **Keywords:** {keywords_str} **MeSH Terms:** {format_mesh_terms(article.mesh_terms)} **Article Types:** {', '.join(article.article_types) if article.article_types else 'Not specified'} **Links:** {links_text} """ return article_text