BioMCP

Instructions

⚠️ 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.

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)