BioMCP

Instructions

Implementation Reference

• src/biomcp/individual_tools.py:756-791 (handler)

  Primary MCP tool handler for 'disease_getter'. Registers the tool with @mcp_app.tool(), defines input schema via Annotated Field, and delegates execution to _disease_details helper.
  @mcp_app.tool() @track_performance("biomcp.disease_getter") async def disease_getter( disease_id_or_name: Annotated[ str, Field( description="Disease name (e.g., 'melanoma', 'lung cancer') or ontology ID (e.g., 'MONDO:0016575', 'DOID:1909')" ), ], ) -> str: """Get detailed disease information from MyDisease.info. ⚠️ PREREQUISITE: Use the 'think' tool FIRST to understand your research goal! Provides real-time disease annotations including: - Official disease name and definition - Disease synonyms and alternative names - Ontology mappings (MONDO, DOID, OMIM, etc.) - Associated phenotypes - Links to disease databases This tool fetches CURRENT disease information from MyDisease.info, ensuring you always have the latest ontology mappings and definitions. Example usage: - Get the definition of GIST (Gastrointestinal Stromal Tumor) - Look up synonyms for melanoma - Find the MONDO ID for a disease by name Note: For clinical trials about diseases, use trial_searcher. For articles about diseases, use article_searcher. """ return await _disease_details( call_benefit="Get up-to-date disease definitions and ontology information", disease_id_or_name=disease_id_or_name, )
• src/biomcp/diseases/getter.py:86-143 (handler)

  Core handler function that performs the actual API query to MyDisease.info via BioThingsClient, formats the result with links and summaries, and returns markdown or JSON.
  async def get_disease( disease_id_or_name: str, output_json: bool = False, ) -> str: """ Get disease information from MyDisease.info. Args: disease_id_or_name: Disease ID (MONDO, DOID) or name (e.g., "melanoma", "MONDO:0016575") output_json: Return as JSON instead of markdown Returns: Disease information as markdown or JSON string """ client = BioThingsClient() try: disease_info = await client.get_disease_info(disease_id_or_name) if not disease_info: error_data = { "error": f"Disease '{disease_id_or_name}' not found", "suggestion": "Please check the disease name or ID (MONDO:, DOID:, OMIM:, MESH:)", } return ( json.dumps(error_data, indent=2) if output_json else to_markdown([error_data]) ) # Convert to dict for rendering result = disease_info.model_dump(exclude_none=True) # Add helpful links _add_disease_links(disease_info, result) # Format output for display _format_disease_output(disease_info, result) if output_json: return json.dumps(result, indent=2) else: return to_markdown([result]) except Exception as e: logger.error( f"Error fetching disease info for {disease_id_or_name}: {e}" ) error_data = { "error": "Failed to retrieve disease information", "details": str(e), } return ( json.dumps(error_data, indent=2) if output_json else to_markdown([error_data]) )
• src/biomcp/diseases/getter.py:145-177 (helper)

  Intermediate helper function called by the MCP tool handler. Includes detailed tool description and calls the core get_disease function.
  async def _disease_details( call_benefit: Annotated[ str, "Define and summarize why this function is being called and the intended benefit", ], disease_id_or_name: Annotated[ str, Field( description="Disease name (e.g., melanoma, GIST) or ID (e.g., MONDO:0016575, DOID:1909)" ), ], ) -> str: """ Retrieves detailed information for a disease from MyDisease.info. This tool provides real-time disease annotations including: - Official disease name and definition - Disease synonyms and alternative names - Ontology mappings (MONDO, DOID, OMIM, etc.) - Associated phenotypes - Links to disease databases Parameters: - call_benefit: Define why this function is being called - disease_id_or_name: Disease name or ontology ID Process: Queries MyDisease.info API for up-to-date disease information Output: Markdown formatted disease information with definition and metadata Note: For clinical trials about diseases, use trial_searcher. For articles about diseases, use article_searcher. """ return await get_disease(disease_id_or_name, output_json=False)
• src/biomcp/diseases/getter.py:15-55 (helper)

  Helper function that adds useful external links (MONDO Browser, Disease Ontology, PubMed) to the disease result dictionary.
  def _add_disease_links(disease_info, result: dict) -> None: """Add helpful links to disease result.""" links = {} # Add MONDO browser link if available if ( disease_info.mondo and isinstance(disease_info.mondo, dict) and (mondo_id := disease_info.mondo.get("mondo")) and isinstance(mondo_id, str) and mondo_id.startswith("MONDO:") ): links["MONDO Browser"] = ( f"https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http://purl.obolibrary.org/obo/{mondo_id.replace(':', '_')}" ) # Add Disease Ontology link if available if ( disease_info.xrefs and isinstance(disease_info.xrefs, dict) and (doid := disease_info.xrefs.get("doid")) ): if isinstance(doid, list) and doid: doid_id = doid[0] if isinstance(doid[0], str) else str(doid[0]) links["Disease Ontology"] = ( f"https://www.disease-ontology.org/?id={doid_id}" ) elif isinstance(doid, str): links["Disease Ontology"] = ( f"https://www.disease-ontology.org/?id={doid}" ) # Add PubMed search link if disease_info.name: links["PubMed Search"] = ( f"https://pubmed.ncbi.nlm.nih.gov/?term={disease_info.name.replace(' ', '+')}" ) if links: result["_links"] = links
• src/biomcp/diseases/getter.py:57-85 (helper)

  Helper function that formats synonyms (truncated list) and associated phenotypes for clean display in the output.
  def _format_disease_output(disease_info, result: dict) -> None: """Format disease output for display.""" # Format synonyms nicely if disease_info.synonyms: result["synonyms"] = ", ".join( disease_info.synonyms[:10] ) # Limit to first 10 if len(disease_info.synonyms) > 10: result["synonyms"] += ( f" (and {len(disease_info.synonyms) - 10} more)" ) # Format phenotypes if present if disease_info.phenotypes: # Just show count and first few phenotypes phenotype_names = [] for pheno in disease_info.phenotypes[:5]: if isinstance(pheno, dict) and "phenotype" in pheno: phenotype_names.append(pheno["phenotype"]) if phenotype_names: result["associated_phenotypes"] = ", ".join(phenotype_names) if len(disease_info.phenotypes) > 5: result["associated_phenotypes"] += ( f" (and {len(disease_info.phenotypes) - 5} more)" ) # Remove the raw phenotypes data for cleaner output result.pop("phenotypes", None)