BioMCP

Instructions

Implementation Reference

• src/biomcp/individual_tools.py:132-160 (handler)

  MCP tool registration and handler function for 'article_getter'. Defines input schema via Annotated Field and delegates execution to _article_details.
  @mcp_app.tool() @track_performance("biomcp.article_getter") async def article_getter( pmid: Annotated[ str, Field( description="Article identifier - either a PubMed ID (e.g., '38768446' or 'PMC11193658') or DOI (e.g., '10.1101/2024.01.20.23288905')" ), ], ) -> str: """Fetch detailed information for a specific article. Retrieves the full abstract and available text for an article by its identifier. Supports: - PubMed IDs (PMID) for published articles - PMC IDs for articles in PubMed Central - DOIs for preprints from Europe PMC Returns formatted text including: - Title - Abstract - Full text (when available from PMC for published articles) - Source information (PubMed or Europe PMC) """ return await _article_details( call_benefit="Fetch detailed article information for analysis", pmid=pmid, )
• src/biomcp/articles/fetch.py:210-252 (helper)

  Core helper function implementing the article fetching logic. Determines if PMID or DOI and calls appropriate APIs (PubTator3 or Europe PMC).
  async def _article_details( call_benefit: Annotated[ str, "Define and summarize why this function is being called and the intended benefit", ], pmid, ) -> str: """ Retrieves details for a single article given its identifier. Parameters: - call_benefit: Define and summarize why this function is being called and the intended benefit - pmid: An article identifier - either a PubMed ID (e.g., 34397683) or DOI (e.g., 10.1101/2024.01.20.23288905) Process: - For PMIDs: Calls the PubTator3 API to fetch the article's title, abstract, and full text (if available) - For DOIs: Calls Europe PMC API to fetch preprint details Output: A JSON formatted string containing the retrieved article content. """ identifier = str(pmid) # Check if it's a DOI (Europe PMC preprint) if is_doi(identifier): from .preprints import fetch_europe_pmc_article return await fetch_europe_pmc_article(identifier, output_json=True) # Check if it's a PMID (PubMed article) elif is_pmid(identifier): return await fetch_articles( [int(identifier)], full=True, output_json=True ) else: # Unknown identifier format return json.dumps( [ { "error": f"Invalid identifier format: {identifier}. Expected either a PMID (numeric) or DOI (10.xxxx/xxxx format)." } ], indent=2, )
• src/biomcp/articles/fetch.py:61-128 (schema)

  Pydantic models defining the structure of fetched article data, including computed fields for title, abstract, full_text, and URLs.
  class Article(BaseModel): pmid: int | None = Field( None, description="PubMed ID of the reference article.", ) pmcid: str | None = Field( None, description="PubMed Central ID of the reference article.", ) date: str | None = Field( None, description="Date of the reference article's publication.", ) journal: str | None = Field( None, description="Journal name.", ) authors: list[str] | None = Field( None, description="List of authors.", ) passages: list[Passage] = Field( ..., alias="passages", description="List of passages in the reference article.", exclude=True, ) @computed_field def title(self) -> str: lines = [] for passage in filter(lambda p: p.is_title, self.passages): if passage.text: lines.append(passage.text) return " ... ".join(lines) or f"Article: {self.pmid}" @computed_field def abstract(self) -> str: lines = [] for passage in filter(lambda p: p.is_abstract, self.passages): if passage.text: lines.append(passage.text) return "\n\n".join(lines) or f"Article: {self.pmid}" @computed_field def full_text(self) -> str: lines = [] for passage in filter(lambda p: p.is_text, self.passages): if passage.text: lines.append(passage.text) return "\n\n".join(lines) or "" @computed_field def pubmed_url(self) -> str | None: url = None if self.pmid: url = f"https://pubmed.ncbi.nlm.nih.gov/{self.pmid}/" return url @computed_field def pmc_url(self) -> str | None: """Generates the PMC URL if PMCID exists.""" url = None if self.pmcid: url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/{self.pmcid}/" return url
• src/biomcp/articles/fetch.py:164-195 (helper)

  Helper function that calls PubTator3 API to fetch article full text and handles response formatting.
  async def fetch_articles( pmids: list[int], full: bool, output_json: bool = False, ) -> str: """Fetch the text of a list of PubMed IDs.""" response, error = await call_pubtator_api(pmids, full) # PubTator API returns full text even when full=False exclude_fields = {"full_text"} if not full else set() # noinspection DuplicatedCode if error: data: list[dict[str, Any]] = [ {"error": f"Error {error.code}: {error.message}"} ] else: data = [ article.model_dump( mode="json", exclude_none=True, exclude=exclude_fields, ) for article in (response.articles if response else []) ] if data and not output_json: return render.to_markdown(data) else: return json.dumps(data, indent=2)