get_data
Retrieve biological data from Biomart by specifying attributes and filters, returning results in CSV format. Use this tool to query datasets efficiently and apply custom filters for targeted data extraction.
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
| Name | Required | Description | Default |
|---|---|---|---|
| attributes | Yes | ||
| dataset | Yes | ||
| filters | Yes | ||
| mart | Yes |
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"
}