mcp-pubmed

Instructions

Implementation Reference

• main.py:374-442 (handler)

  Implementation of the `get_article` tool handler using the FastMCP decorator. It takes a PMID as input, queries the NCBI E-utilities API, and formats the response.

  @mcp.tool()
  async def get_article(pmid: str) -> str:
      """Get complete details of a PubMed article by its PMID.
  
      Args:
          pmid: The PubMed ID (numeric string), e.g. "33982811".
  
      Returns:
          Full article metadata: title, all authors, journal, date, DOI,
          PMC link, publication types, full abstract, keywords, MeSH terms.
          Returns an error message if the PMID is invalid or not found.
      """
      pmid = pmid.strip()
      if not pmid.isdigit():
          return _err(f"Invalid PMID: {pmid!r}. A PMID must be a numeric string.")
  
      try:
          fetch_resp = await _get(
              "efetch.fcgi",
              {"db": "pubmed", "id": pmid, "retmode": "xml", "rettype": "abstract"},
          )
          root = _require_xml(fetch_resp, f"efetch PMID {pmid}")
          article_xml = root.find(".//PubmedArticle")
  
          if article_xml is None:
              return _err(f"No article found for PMID {pmid}. It may not exist or may have been retracted.")
  
          art = _parse_article(article_xml)
  
          lines = [f"=== PubMed Article — PMID {pmid} ==="]
          lines.append(f"Title    : {art.get('title', 'N/A')}")
  
          authors = art.get("authors", [])
          if authors:
              lines.append(f"Authors  : {', '.join(authors)}")
  
          lines.append(f"Journal  : {art.get('journal', 'N/A')}")
          lines.append(f"Published: {art.get('pub_date', 'N/A')}")
  
          if "doi" in art:
              lines.append(f"DOI      : {art['doi']}")
              lines.append(f"DOI URL  : https://doi.org/{art['doi']}")
  
          if "pmc_id" in art:
              pmc_id = art["pmc_id"]
              lines.append(f"PMC ID   : {pmc_id}")
              lines.append(f"PMC URL  : https://www.ncbi.nlm.nih.gov/pmc/articles/{pmc_id}/")
  
          lines.append(f"PubMed   : https://pubmed.ncbi.nlm.nih.gov/{pmid}/")
  
          if "publication_types" in art:
              lines.append(f"Type(s)  : {', '.join(art['publication_types'])}")
  
          if "abstract" in art:
              lines.append(f"\nAbstract:\n{art['abstract']}")
          else:
              lines.append("\nAbstract: Not available.")
  
          if "keywords" in art:
              lines.append(f"\nKeywords : {', '.join(art['keywords'])}")
  
          if "mesh_terms" in art:
              lines.append(f"\nMeSH     : {', '.join(art['mesh_terms'])}")
  
          return "\n".join(lines)
  
      except PubMedError as exc:
          return _err(str(exc))