Interface with Biomart databases to discover marts, datasets, and retrieve biological data efficiently. Utilize tools for attribute exploration and ID translation to enhance your data analysis capabilities. Streamline your biological data queries with a standardized MCP server.
Tools
list_marts
Lists all available Biomart marts (databases) from Ensembl. Biomart organizes biological data in a hierarchy: MART -> DATASET -> ATTRIBUTES/FILTERS. This function returns all available marts as a CSV string. Returns: str: CSV-formatted table of all marts with their display names and descriptions. Example: list_marts() >>> "name,display_name,description ENSEMBL_MART_ENSEMBL,Ensembl Genes,Gene annotation from Ensembl ENSEMBL_MART_MOUSE,Mouse strains,Strain-specific data for mouse ..."
list_datasets
Lists all available biomart datasets for a given mart. Each mart contains multiple datasets. This function returns all datasets available in the specified mart as a CSV string. Args: mart (str): The mart identifier to list datasets from. Valid values include: ENSEMBL_MART_ENSEMBL, ENSEMBL_MART_MOUSE, ENSEMBL_MART_ONTOLOGY, ENSEMBL_MART_GENOMIC, ENSEMBL_MART_SNP, ENSEMBL_MART_FUNCGEN Returns: str: CSV-formatted table of all datasets with their display names and descriptions. Example: list_datasets("ENSEMBL_MART_ENSEMBL") >>> "name,display_name,description hsapiens_gene_ensembl,Human genes,Human genes (GRCh38.p13) mmusculus_gene_ensembl,Mouse genes,Mouse genes (GRCm39) ..."
list_common_attributes
Lists commonly used attributes available for a given dataset. This function returns only the most frequently used attributes (defined in COMMON_ATTRIBUTES) to avoid overwhelming the model with too many options. For a complete list, use list_all_attributes. Args: mart (str): The mart identifier (e.g., "ENSEMBL_MART_ENSEMBL") dataset (str): The dataset identifier (e.g., "hsapiens_gene_ensembl") Returns: str: CSV-formatted table of common attributes with their display names and descriptions. Example: list_common_attributes("ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl") >>> "name,display_name,description ensembl_gene_id,Gene stable ID,Ensembl stable ID for the gene external_gene_name,Gene name,The gene name ..."
list_all_attributes
Lists all available attributes for a given dataset with some filtering. This function returns a filtered list of all attributes available for the specified dataset. Some less commonly used attributes (homologs, microarray probes) are filtered out to reduce the response size. CAUTION: This function can return a large number of attributes and may be unstable for certain datasets. Consider using list_common_attributes first. Args: mart (str): The mart identifier (e.g., "ENSEMBL_MART_ENSEMBL") dataset (str): The dataset identifier (e.g., "hsapiens_gene_ensembl") Returns: str: CSV-formatted table of all filtered attributes. Example: list_all_attributes("ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl")
Installation
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