get_translation
Convert biological identifiers, such as gene symbols to Ensembl IDs, using Biomart MCP. Specify source and target attributes to retrieve translated results quickly with caching for efficiency.
Instructions
Translates a single identifier from one attribute type to another.
This function allows conversion between different identifier types, such as
converting a gene symbol to an Ensembl ID. Results are cached to improve performance.
Args:
mart (str): The mart identifier (e.g., "ENSEMBL_MART_ENSEMBL")
dataset (str): The dataset identifier (e.g., "hsapiens_gene_ensembl")
from_attr (str): The source attribute name (e.g., "hgnc_symbol")
to_attr (str): The target attribute name (e.g., "ensembl_gene_id")
target (str): The identifier value to translate (e.g., "TP53")
Returns:
str: The translated identifier, or an error message if not found.
Example:
get_translation("ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl", "hgnc_symbol", "ensembl_gene_id", "TP53")
>>> "ENSG00000141510"Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| dataset | Yes | ||
| from_attr | Yes | ||
| mart | Yes | ||
| target | Yes | ||
| to_attr | Yes |
Implementation Reference
- biomart-mcp.py:273-304 (handler)The complete handler function for the 'get_translation' MCP tool, including the @mcp.tool() decorator, type hints, docstring schema, and execution logic. It retrieves a cached translation dictionary and looks up the target identifier.
@mcp.tool() def get_translation(mart: str, dataset: str, from_attr: str, to_attr: str, target: str): """ Translates a single identifier from one attribute type to another. This function allows conversion between different identifier types, such as converting a gene symbol to an Ensembl ID. Results are cached to improve performance. Args: mart (str): The mart identifier (e.g., "ENSEMBL_MART_ENSEMBL") dataset (str): The dataset identifier (e.g., "hsapiens_gene_ensembl") from_attr (str): The source attribute name (e.g., "hgnc_symbol") to_attr (str): The target attribute name (e.g., "ensembl_gene_id") target (str): The identifier value to translate (e.g., "TP53") Returns: str: The translated identifier, or an error message if not found. Example: get_translation("ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl", "hgnc_symbol", "ensembl_gene_id", "TP53") >>> "ENSG00000141510" """ try: result_dict = _get_translation_dict(mart, dataset, from_attr, to_attr) if target not in result_dict: print(f"Target '{target}' not found in translation", file=sys.stderr) return f"Error: Target '{target}' not found" return result_dict[target] except Exception as e: print(f"Error in translation: {str(e)}", file=sys.stderr) return f"Error: {str(e)}" - biomart-mcp.py:259-271 (helper)Supporting helper function _get_translation_dict, cached with lru_cache, that queries Biomart to create a dictionary mapping values from 'from_attr' to 'to_attr'. Used by get_translation and batch_translate tools.
def _get_translation_dict(mart: str, dataset: str, from_attr: str, to_attr: str): """ Helper function to get and cache a translation dictionary. """ try: server = get_server() dataset_obj = server[mart][dataset] df = dataset_obj.query(attributes=[from_attr, to_attr]) return dict(zip(df.iloc[:, 0], df.iloc[:, 1])) except Exception as e: print(f"Error getting translation dictionary: {str(e)}", file=sys.stderr) return {}