BioContextAI Knowledgebase MCP

Instructions

Implementation Reference

• src/biocontext_kb/core/panglaodb/_get_panglaodb_options.py:7-25 (handler)

  The primary handler function for the get_panglaodb_options tool (likely referred to as bc_get_panglaodb_options externally). It fetches unique organ and cell_type filter options from the PanglaoDB dataset using a helper function.
  @core_mcp.tool() def get_panglaodb_options() -> Dict[str, List[str] | str]: """Retrieve available filter options for PanglaoDB marker genes. Returns unique values for organs and cell types. Returns: dict: Lists of unique organ and cell_type values available in PanglaoDB dataset or error message. """ panglao_db_df = get_panglaodb_df() if panglao_db_df is None: return {"error": "PanglaoDB data is not loaded. Check server logs."} # Get unique values for each column, handling NaN values organ = panglao_db_df["organ"].dropna().str.lower().unique().tolist() cell_type = panglao_db_df["cell type"].dropna().str.lower().unique().tolist() return { "organ": organ, "cell_type": cell_type, }
• src/biocontext_kb/core/panglaodb/_get_panglaodb_df.py:6-27 (helper)

  Supporting helper function that loads the PanglaoDB marker genes TSV file into a pandas DataFrame, used by the main handler.
  def get_panglaodb_df() -> pd.DataFrame | None: """Load the PanglaoDB dataset into a pandas DataFrame. Returns: pd.DataFrame | None: The loaded DataFrame or None if loading fails. """ # Construct the path to the TSV file panglao_db_path = Path(__file__).parent / "data" / "PanglaoDB_markers_27_Mar_2020.tsv" # Load the database into a pandas DataFrame try: panglao_db_df = pd.read_csv(panglao_db_path, sep="\t", engine="python", header=0) # Replace empty strings and other potential non-values with NaN for consistency panglao_db_df = panglao_db_df.replace("", pd.NA) return panglao_db_df except FileNotFoundError: print(f"Error: PanglaoDB file not found at {panglao_db_path}") return None except Exception as e: print(f"Error loading PanglaoDB file: {e}") return None
• src/biocontext_kb/core/__init__.py:15-15 (registration)

  Import statement in core/__init__.py that triggers the import and registration of panglaodb tools via their decorators when the module is loaded.
  from .panglaodb import *
• src/biocontext_kb/core/panglaodb/__init__.py:2-2 (registration)

  Re-exports the tool handler function, allowing it to be imported and registered via panglaodb.__init__.
  from ._get_panglaodb_options import get_panglaodb_options