Biomart MCP

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"

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 {}