bc_get_efo_id_by_disease_name
Retrieve EFO, Mondo, or HP ontology IDs for a specific disease name by querying the Ontology Lookup Service. Supports customizable search parameters for exact matches and result limits.
Instructions
Query the Ontology Lookup Service (OLS) for EFO/Mondo/HP IDs related to a disease name.
This function searches for EFO IDs associated with a given disease name using the OLS API. Always use this function if you need EFO IDs, e.g., for use in the Open Targets API.
Args: disease_name (str): The name of the disease to search for (e.g., "SIDS"). size (int): Maximum number of results to return (default: 5). exact_match (bool): Whether to perform an exact match search (default: False).
Returns: dict: Dictionary containing EFO IDs and information or error message
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| disease_name | Yes | The name of the disease to search for (e.g., 'choledocholithiasis') | |
| exact_match | No | Whether to perform an exact match search | |
| size | No | The maximum number of results to return |
Implementation Reference
- The core handler function for the 'bc_get_efo_id_by_disease_name' tool. It queries the OLS API (https://www.ebi.ac.uk/ols4/api/v2/entities) for EFO, MONDO, or HP terms matching the disease name, filters valid prefixes, and returns a list of IDs with labels and descriptions or an error.@core_mcp.tool() def get_efo_id_by_disease_name( disease_name: Annotated[str, Field(description="Disease name to search for (e.g., 'choledocholithiasis')")], size: Annotated[ int, Field(description="Maximum number of results to return"), ] = 5, exact_match: Annotated[ bool, Field(description="Whether to perform exact match search"), ] = False, ) -> Dict[str, Any]: """Search OLS for EFO/Mondo/HP IDs related to a disease name. Use this to get EFO IDs for Open Targets queries. Returns: dict: EFO IDs with efo_ids array containing id, label, description or error message. """ if not disease_name: return {"error": "disease_name must be provided"} url = "https://www.ebi.ac.uk/ols4/api/v2/entities" params = { "search": disease_name, "size": str(size), "lang": "en", "exactMatch": str(exact_match).lower(), "includeObsoleteEntities": "false", "ontologyId": "efo", } def starts_with_valid_prefix(curie: str) -> bool: """Check if the curie starts with a valid prefix.""" return any(curie.startswith(prefix) for prefix in ["EFO:", "MONDO:", "HP:"]) try: response = requests.get(url, params=params) response.raise_for_status() data = response.json() # Check that at least one item is in elements and that appearsIn includes EFO if not data.get("elements") or not any( starts_with_valid_prefix(str(element.get("curie", ""))) for element in data["elements"] ): return {"error": "No results found"} # Extract EFO IDs and their labels efo_ids = [ { "id": element["curie"].replace(":", "_"), "label": element["label"], "description": element.get("description", ""), } for element in data["elements"] if starts_with_valid_prefix(str(element.get("curie", ""))) ] return {"efo_ids": efo_ids} except requests.exceptions.RequestException as e: return {"error": f"Failed to fetch EFO IDs: {e!s}"}