Biomart MCP

MIT License
1
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get_data

Retrieve biological data from Biomart using specific attributes and filters. Specify dataset, mart, desired attributes, and filters to query and obtain results in CSV format.

Instructions

Queries Biomart for data using specified attributes and filters. This function performs the main data retrieval from Biomart, allowing you to query biological data by specifying which attributes to return and which filters to apply. Includes automatic retry logic for resilience. Args: mart (str): The mart identifier (e.g., "ENSEMBL_MART_ENSEMBL") dataset (str): The dataset identifier (e.g., "hsapiens_gene_ensembl") attributes (list[str]): List of attributes to retrieve (e.g., ["ensembl_gene_id", "external_gene_name"]) filters (dict[str, str]): Dictionary of filters to apply (e.g., {"chromosome_name": "1"}) Returns: str: CSV-formatted results of the query. Example: get_data( "ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl", ["ensembl_gene_id", "external_gene_name", "chromosome_name"], {"chromosome_name": "X", "biotype": "protein_coding"} ) >>> "ensembl_gene_id,external_gene_name,chromosome_name ENSG00000000003,TSPAN6,X ENSG00000000005,TNMD,X ..."

Input Schema

NameRequiredDescriptionDefault
attributesYes
datasetYes
filtersYes
martYes

Input Schema (JSON Schema)

{ "properties": { "attributes": { "items": { "type": "string" }, "title": "Attributes", "type": "array" }, "dataset": { "title": "Dataset", "type": "string" }, "filters": { "additionalProperties": { "type": "string" }, "title": "Filters", "type": "object" }, "mart": { "title": "Mart", "type": "string" } }, "required": [ "mart", "dataset", "attributes", "filters" ], "title": "get_dataArguments", "type": "object" }

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