BioMCP

Instructions

Implementation Reference

• src/biomcp/drugs/getter.py:145-162 (handler)

  Core MCP tool handler function _drug_details that executes the drug retrieval logic
  async def _drug_details(drug_id_or_name: str) -> str: """Get drug/chemical information from MyChem.info. This tool retrieves comprehensive drug information including: - Drug identifiers (DrugBank, ChEMBL, PubChem, etc.) - Chemical properties (formula, InChIKey) - Trade names and synonyms - Clinical indications - Mechanism of action - Links to external databases Args: drug_id_or_name: Drug name (e.g., "aspirin") or ID (e.g., "DB00945", "CHEMBL25") Returns: Formatted drug information with external database links """ return await get_drug(drug_id_or_name, output_json=False)
• src/biomcp/drugs/getter.py:103-142 (handler)

  Primary get_drug function that fetches data from MyChem.info API, formats output, and handles errors
  async def get_drug(drug_id_or_name: str, output_json: bool = False) -> str: """Get drug information from MyChem.info. Args: drug_id_or_name: Drug ID (DrugBank, ChEMBL, etc.) or name output_json: Return JSON instead of formatted text Returns: Formatted drug information or JSON string """ try: client = BioThingsClient() drug_info = await client.get_drug_info(drug_id_or_name) if not drug_info: error_msg = f"Drug '{drug_id_or_name}' not found in MyChem.info" if output_json: return json.dumps({"error": error_msg}, indent=2) return error_msg # Build result dictionary result = drug_info.model_dump(by_alias=False, exclude_none=True) # Add external links _add_drug_links(drug_info, result) if output_json: return json.dumps(result, indent=2) # Format for text output _format_drug_output(drug_info, result) return result["_formatted"] except Exception as e: logger.error(f"Error getting drug info: {e}") error_msg = f"Error retrieving drug information: {e!s}" if output_json: return json.dumps({"error": error_msg}, indent=2) return error_msg
• src/biomcp/individual_tools.py:793-827 (registration)

  MCP tool registration for 'drug_getter' including input schema definition and docstring; wraps internal _drug_details handler
  @mcp_app.tool() @track_performance("biomcp.drug_getter") async def drug_getter( drug_id_or_name: Annotated[ str, Field( description="Drug name (e.g., 'aspirin', 'imatinib') or ID (e.g., 'DB00945', 'CHEMBL941')" ), ], ) -> str: """Get detailed drug/chemical information from MyChem.info. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to understand your research goal! This tool provides comprehensive drug information including: - Chemical properties (formula, InChIKey) - Drug identifiers (DrugBank, ChEMBL, PubChem) - Trade names and brand names - Clinical indications - Mechanism of action - Pharmacology details - Links to drug databases This tool fetches CURRENT drug information from MyChem.info, part of the BioThings suite, ensuring you always have the latest drug data. Example usage: - Get information about imatinib (Gleevec) - Look up details for DrugBank ID DB00619 - Find the mechanism of action for pembrolizumab Note: For clinical trials about drugs, use trial_searcher. For articles about drugs, use article_searcher. """ return await _drug_details(drug_id_or_name)
• src/biomcp/individual_tools.py:796-801 (schema)

  Pydantic input schema definition for drug_getter tool parameter using Annotated and Field
  drug_id_or_name: Annotated[ str, Field( description="Drug name (e.g., 'aspirin', 'imatinib') or ID (e.g., 'DB00945', 'CHEMBL941')" ), ],
• src/biomcp/drugs/getter.py:88-101 (helper)

  Helper function to format drug information into markdown text output with sections and links
  def _format_drug_output(drug_info, result: dict) -> None: """Format drug information for text output.""" output_lines = [f"## Drug: {drug_info.name or 'Unknown'}"] _format_basic_info(drug_info, output_lines) _format_clinical_info(drug_info, output_lines) if result.get("_links"): output_lines.append("\n### External Links") for name, url in result["_links"].items(): output_lines.append(f"- [{name}]({url})") result["_formatted"] = "\n".join(output_lines)